Microbiome Archive/Intro
Probiotic-specific archive: /s/HumanMicrobiome/wiki/probiotics
For feedback, edits, contributions, suggestions, etc. please use the current stickied meta thread.
sci-hub.tw can be used to bypass paywalls.
If you're curious about a condition not listed here, do a google, pubmed, or google scholar search for "condition microbiome" or "condition dysbiosis".
Research in the area of the microbiome is growing rapidly in recent years due to advances in detection/sequencing techniques: https://microbiomedigestdotcom.files.wordpress.com/2017/01/2000-2016-graph-pubmed.png?w=869 - this means that many long standing positions are being debunked, and even much of what you read (here or elsewhere) can become quickly outdated.
See this testing section for examples of current status/limitations of detecting & identifying human microbes: https://old.reddit.com/s/HumanMicrobiome/wiki/index#wiki_testing.3A
General articles:
Fantastic microbiome 101 podcast by Yale: https://soundcloud.com/yaleuniversity/microbiome-episode-i || Other parts of series (not as good/accurate): https://archive.is/LPh4d
Excellent 2018 PBS NOVA documentary: NOVA Wonders What's Living in You? http://www.pbs.org/video/nova-wonders-whats-living-in-you-fnbfuy/
Kurzgesagt – How Bacteria Rule Over Your Body – The Microbiome https://www.youtube.com/watch?v=VzPD009qTN4 - A good, simple intro, but some things might be wrong/outdated.
Ed Yong's 2016 "I contain multitudes" book is excellent.
And Martin Blaser's (2014) "Missing Microbes". Discussion, interviews, summary.
"It is now clear that the gut microbiota contributes significantly to the traits of humans as much as our genes, especially in the case of atherosclerosis, hypertension, obesity, diabetes, metabolic syndrome, inflammatory bowel disease (IBD), gastrointestinal tract malignancies, hepatic encephalopathy, allergies, behavior, intelligence, autism, neurological diseases, and psychological diseases. It has also been found that alteration of the composition of the gut microbiota in its host affects the behavior, intelligence, mood, autism, psychology, and migraines of its host through the gut-brain axis." (2018): https://www.frontiersin.org/articles/10.3389/fmicb.2018.01510/full
How the Western Diet (and antimicrobials) Has Derailed Our Evolution (2015): http://nautil.us//issue/30/identity/how-the-western-diet-has-derailed-our-evolution
Is a Disrupted Gut Microbiome at the Root of Modern Disease? (2016) https://chriskresser.com/is-a-disrupted-gut-microbiome-at-the-root-of-modern-disease-with-dr-justin-sonnenburg/
Meet Your Second Brain: The Gut (2015) http://www.mindful.org/meet-your-second-brain-the-gut/
How the Gut's "Second Brain" Influences Mood and Well-Being. The emerging and surprising view of how the enteric nervous system in our bellies goes far beyond just processing the food we eat (2010): https://www.scientificamerican.com/article/gut-second-brain/
Documentary: In Defense of Food, http://www.pbs.org/video/2365635287/ 1:25:00 talks about study in twins where one is malnurished and one isn't. Bacteria transplant tests. Also testing gut microbes in Hanza tribe. || Also talked about during the 2016 whitehouse microbiome event: https://www.youtube.com/watch?v=q3xS-kXINLc&t=1h38m
A group of scientists have found that a single molecule from a bacterial cell wall component can lead to the unusual behaviour of 100 million clotting molecules in blood, which may be a major contributor to many diseases including Alzheimer's, Parkinson's, diabetes, rheumatoid arthritis, & strokes: http://www.bbsrc.ac.uk/news/health/2016/160907-pr-link-between-bacteria-and-non-infectious-diseases/ || Related: The dormant blood microbiome in chronic, inflammatory diseases (2015): https://academic.oup.com/femsre/article/39/4/567/2467761
Alzheimer's, cancer and other incurable diseases such as Parkinson's and dementia can be contagious (via phages): http://www.prnewswire.com/news-releases/new-research-indicates-alzheimers-and-other-neurodegenerative-diseases-are-contagious-300333155.html - http://hmi-us.com/newsroom/news-from-the-hmi/httpswww-accesswire-com478028ny-scientists-first-to-link-neurodegenerative-diseases-and-bacterial-viruses.html
How gut bacteria affects your health: What we know, what we don't (2015): http://www.mprnews.org/story/2015/06/09/bcst-microbes-gut-bacteria
11 overlooked factors that affect the bacteria on your body and help determine your health (2015): http://www.businessinsider.com/what-affects-your-microbiome-2015-11
How gut bacteria affect the brain and body (2015): http://big.assets.huffingtonpost.com/2015_GutBacteriaA.png
9 fascinating facts about the microbiome (2015) (birthing section is wrong on sterility): http://www.fastcoexist.com/3053260/9-fascinating-facts-about-the-microbiome-the-trillions-of-microbes-hidden-inside-us
Fantastic site for keeping up with the latest literature; run by Stanford researcher: http://www.microbiomedigest.com/
Aging/longevity:
Brain function:
Gut bacteria produce and consume neurotransmitters: https://archive.is/IU5e3 - https://www.sciencedirect.com/science/article/pii/S0006899318301501 - Along with gasotransmitters that affect our brain, mind and behavior: https://archive.is/zeo4s || As do gut fungi: http://www.mdpi.com/2076-2607/6/1/22/htm
Gut microbes regulate serotonin: http://www.sci-news.com/medicine/gut-microbiota-physiology-04500.html
Microbial Genes, Brain & Behaviour - Epigenetic Regulation of the Gut-Brain Axis: To date, there is rapidly increasing evidence for host-microbe interaction on virtually all levels of complexity, ranging from direct cell-to-cell communication to extensive systemic signalling, and involving various organs and organ systems, including the central nervous system. As such, the discovery that differential microbial composition is associated with alterations in behavior and cognition has significantly contributed to establish the microbiota-gut-brain axis as an extension of the well-accepted gut-brain axis concept. (2013) https://www.researchgate.net/publication/259001830_Microbial_Genes_Brain_Behaviour_-_Epigenetic_Regulation_of_the_Gut-Brain_Axis
Gut bacteria regulate nerve fibre insulation. Research suggests that gut bacteria may directly affect brain structure and function, offering new ways to treat multiple sclerosis and psychiatric conditions (2016): https://www.theguardian.com/science/neurophilosophy/2016/apr/05/gut-bacteria-brain-myelin
Gut bacteria essential for neurogenesis; Antibiotics that kill gut bacteria also stop growth of new brain cells: http://www.cell.com/cell-reports/fulltext/S2211-1247%2816%2930518-6 - https://www.sciencedaily.com/releases/2016/05/160519130105.htm
Neuron destruction processes in the brain could be triggered by proteins produced by gut microbiota: http://www.ctvnews.ca/health/gut-microbiota-may-have-role-in-neurodegenerative-diseases-study-1.3107349
The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice: http://www.ncbi.nlm.nih.gov/pubmed/21683077
The adoptive transfer of behavioral phenotype via the intestinal microbiota: experimental evidence and clinical implications (2013): https://doi.org/10.1016/j.mib.2013.06.004 "raising the possibility of using FMT for disorders of the central nervous system, and prompting caution in the selection of FMT donors"
Correlation between gut microbiota and personality in adults: A cross-sectional study (2017): https://www.sciencedirect.com/science/article/pii/S0889159117305536
The Virus That Could Cure Alzheimer’s, Parkinson’s, and More: http://www.pbs.org/wgbh/nova/next/body/phage-alzheimers-cure/
Gut microbiome populations are associated with structure-specific changes in white matter architecture (2018): https://www.nature.com/articles/s41398-017-0022-5
Review, 2018: Microbiome—The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health https://www.mdpi.com/2077-0383/7/12/521/htm "mounting data that gut microbiota is the source of a number of neuroactive and immunocompetent substances, which shape the structure and function of brain regions involved in the control of emotions, cognition, and physical activity"
Review, 2018: Microorganisms’ Footprint in Neurodegenerative Diseases https://doi.org/10.3389/fncel.2018.00466 "The negative direct or indirect contributions of various microorganisms in onset or severity of some neurodegeneration disorders and interaction between human immune system and pathogenic microorganisms has been portrayed in this review article"
Review, 2018: The Brain-Gut-Microbiome Axis https://www.cmghjournal.org/article/S2352-345X(18)30060-2/fulltext
Review, 2017: Neuromicrobiology: how microbes influence the brain: http://pubs.acs.org/doi/pdfplus/10.1021/acschemneuro.7b00373 | via sci-hub: http://pubs.acs.org.sci-hub.tw/doi/pdfplus/10.1021/acschemneuro.7b00373
Review, 2017: Gut reactions: How the blood–brain barrier connects the microbiome and the brain: http://journals.sagepub.com/doi/10.1177/1535370217743766
Review, 2017: Feeding the Microbiota-Gut-Brain Axis: Diet, Microbiome and Neuropsychiatry: http://www.sciencedirect.com/science/article/pii/S193152441630264X
Review, 2016: Cognitive Function and the Microbiome, International Review of Neurobiology: http://www.sciencedirect.com/science/article/pii/S0074774216301349
Review, 2015: Serotonin, tryptophan metabolism and the brain-gut-microbiome axis: http://www.sciencedirect.com/science/article/pii/S0166432814004768
Review, 2015: The impact of gut microbiota on brain and behaviour: implications for psychiatry: http://www.ncbi.nlm.nih.gov/pubmed/26372511 - "The current narrative suggests that certain neuropsychiatric disorders might be treated by targeting the microbiota either by microbiota transplantation, antibiotics or psychobiotics."
Review, 2014: The effects of inflammation, infection and antibiotics on the microbiota-gut-brain axis: http://www.ncbi.nlm.nih.gov/pubmed/24997039
Review, 2013: Microbial Endocrinology in the Microbiome-Gut-Brain Axis: How Bacterial Production and Utilization of Neurochemicals Influence Behavior: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003726
Review, 2013: The role of gut microbiota in the gut-brain axis: current challenges and perspectives: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875553/
Review, 2012: The impact of the gut microbiota on brain and behaviour: http://www.ncbi.nlm.nih.gov/pubmed/22968153
Review, 2012: Regulation of the stress response by the gut microbiota: implications for psychoneuroendocrinology: http://www.ncbi.nlm.nih.gov/pubmed/22483040
Review, 2011: The microbiome-gut-brain axis: from bowel to behavior: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2982.2010.01664.x/full
"In conclusion, we demonstrate a molecular basis for how the host microbiome is crucial for a normal behavioural response during social interaction. Our data further suggest that social behaviour is correlated with the gene-expression response in the amygdala, established during neurodevelopment as a result of host-microbe interactions." (2018) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995540/
A new pathway for the gut microbiota to modulate the brain: activation of pattern-recognition receptors by microbial products (peptidoglycan-sensing molecule Pglyrp2) (2017): http://www.nature.com/mp/journal/vaop/ncurrent/full/mp2016182a.html
Microbiota and host determinants of behavioural phenotype in maternally separated mice: http://www.nature.com/ncomms/2015/150728/ncomms8735/full/ncomms8735.html - "MS-induced changes in host physiology lead to intestinal dysbiosis"
Consumption of Fermented Milk Product With Probiotic Modulates Brain Activity: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839572/
Decreased social anxiety among young adults who eat fermented foods: https://www.sciencedaily.com/releases/2015/06/150609092803.htm
Zika, Herpes, and West Nile viruses damage adult brains: https://www.invisiverse.com/news/viruses-might-cause-brain-changes-learning-problems-0177641/ - https://www.washingtonpost.com/news/to-your-health/wp/2017/11/07/new-evidence-of-brain-damage-from-west-nile-virus-scientists-say/ - http://www.pbs.org/wgbh/nova/next/body/zika-might-cause-brain-damage-in-adults-too/ - http://www.cell.com/cell-stem-cell/pdf/S1934-5909(16)30252-1.pdf - https://www.sciencedaily.com/releases/2017/07/170710122959.htm
More in probiotic-specific archive: /s/HumanMicrobiome/wiki/probiotics
ADHD:
ADHD-originating in the gut? The emergence of a new explanatory model (2018): https://doi.org/10.1016/j.mehy.2018.08.022
Alzheimer’s:
Review, 2018: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review: https://link.springer.com/article/10.1007/s12035-018-1188-4
Review, 2018: Microbiome-Mediated Upregulation of MicroRNA-146a in Sporadic Alzheimer’s Disease https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5867462/
Review, 2016: Alzheimer’s disease and gut microbiota: http://link.springer.com/article/10.1007%2Fs11427-016-5083-9
Review, 2016: Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease: http://nutritionreviews.oxfordjournals.org/content/74/10/624
Corroboration of a Major Role for Herpes Simplex Virus Type 1 in Alzheimer’s Disease (2018): https://www.frontiersin.org/articles/10.3389/fnagi.2018.00324/full
Infectious Theory of Alzheimer's Disease Draws Fresh Interest (2018): https://www.npr.org/sections/health-shots/2018/09/09/645629133/infectious-theory-of-alzheimers-disease-draws-fresh-interest
Periodontal disease bacteria may kick-start Alzheimer's. Chronic oral application of a periodontal pathogen results in brain inflammation, neurodegeneration and amyloid beta production in wild type mice (2018): https://medicalxpress.com/news/2018-10-periodontal-disease-bacteria-kick-start-alzheimer.html
A Common Gum Infection Bacteria (P. gingivalis) May Also be Causing Alzheimer’s. Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors (Jan 2019) http://blogs.discovermagazine.com/d-brief/2019/01/23/dental-infection-may-spur-alzheimers-disease
Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? (2018): https://content.iospress.com/articles/journal-of-alzheimers-disease/jad180319
Mapping The Brain's Microbiome: Can Studying Germs In The Brain Lead To A Cure For Alzheimer's? (2017) https://www.forbes.com/sites/robinseatonjefferson/2017/07/28/mapping-the-brains-microbiome-can-studying-germs-in-the-brain-lead-to-a-cure-for-alzheimers/ | Alt links: p1 https://archive.is/vTdFK p2 https://archive.is/8tG5p
Antibiotics weaken Alzheimer's disease progression through changes in the gut microbiome (2016): http://www.eurekalert.org/pub_releases/2016-07/uocm-awa071516.php
Researchers Identify Virus and Two Types of Bacteria as Major Causes of Alzheimer’s (2016). “We are saying there is incontrovertible evidence that Alzheimer’s Disease has a dormant microbial component, and that this can be woken up by iron dysregulation." http://neurosciencenews.com/microbes-alzheimers-neurology-3826/
The gut microbiota-derived metabolite trimethylamine N-oxide [that has been implicated in human disease pathogenesis] is elevated in Alzheimer’s disease (2018): https://doi.org/10.1186/s13195-018-0451-2
Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota (2017): http://www.nature.com/articles/srep41802
Protective Roles of Intestinal Microbiota derived Short Chain Fatty Acids in Alzheimer's Disease-type Beta-Amyloid Neuropathological Mechanisms (2017): https://www.ncbi.nlm.nih.gov/pubmed/29095058
Gut microbiome alterations in Alzheimer’s disease (2017). https://www.nature.com/articles/s41598-017-13601-y
Autism:
Review, 2018: The Perturbance of Microbiome and Gut-Brain Axis in Autism Spectrum Disorders http://www.mdpi.com/1422-0067/19/8/2251/htm
Review, 2018: Early Disruption of the Microbiome Leading to Decreased Antioxidant Capacity and Epigenetic Changes: Implications for the Rise in Autism https://doi.org/10.3389/fncel.2018.00256
Review, 2016: Gut Microbiota and Autism: Key Concepts and Findings: http://link.springer.com/article/10.1007%2Fs10803-016-2960-9
Autism Risk Determined by Health of Mom’s Gut, UVA Research Reveals. "as a result of microflora-associated calibration of gestational IL-17a (inflammatory molecule interleukin-17a) responses" (2018): /r/HumanMicrobiome/comments/906hb9 - Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism (2018) http://www.jimmunol.org/content/early/2018/06/29/jimmunol.1701755
The microbiota modulates gut physiology and behavioral abnormalities associated with autism/neurodevelopmental disorders (2013): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897394/ - http://www.ncbi.nlm.nih.gov/pubmed/24315484
Alteration of gut microbiota-associated epitopes (MEs) in children with autism spectrum disorders (2018): https://doi.org/10.1016/j.bbi.2018.10.006 "thirty-four MEs identified were potential biomarker of ASD, and alterations in MEs may contribute to abnormalities in gut immunity and/or homeostasis in ASD children"
Autism, antibiotics & probiotics: http://jeffreydachmd.com/2015/05/curing-autism-with-antibiotics/ - http://www.healio.com/infectious-disease/pediatric-id/news/online/%7Bf49b2afe-1b1e-4f66-9a3f-ffc9f68b40bf%7D/baylor-investigates-antibiotic-use-childrens-improved-autism-symptoms
A single species of gut bacteria can reverse autism-related social behavior in mice. Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring (2016): https://www.sciencedaily.com/releases/2016/06/160616140723.htm | Nearly identical 2018 follow up study: Mechanisms Underlying Microbial-Mediated Changes in Social Behavior in Mouse Models of Autism Spectrum Disorder http://dx.doi.org/10.1016/j.neuron.2018.11.018
ASU 10 week FMT trial shows improvements (2017): https://autism.asu.edu/ - http://www.readcube.com/articles/10.1186/s40168-016-0225-7
Depression and anxiety:
The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study (2018): https://www.jad-journal.com/article/S0165-0327(18)30193-9/fulltext - FMT improves psych symptoms even when it doesn't change IBS symptoms.
Review, 2018: Gut microbiome and depression: what we know and what we need to know: https://www.degruyter.com/view/j/revneuro.ahead-of-print/revneuro-2017-0072/revneuro-2017-0072.xml
Review, 2018: The Role of Microbiome in Insomnia, Circadian Disturbance and Depression https://www.frontiersin.org/articles/10.3389/fpsyt.2018.00669/full
Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus (2018): https://www.nature.com/articles/s41398-018-0240-5
Microbiota Modulate Anxiety-Like Behavior and Endocrine Abnormalities in Hypothalamic-Pituitary-Adrenal Axis (2017): https://www.frontiersin.org/articles/10.3389/fcimb.2017.00489/full
Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-?B activation through gut microbiota disturbance (2018): https://www.nature.com/articles/s41598-018-31764-0 "However, the amelioration of gastrointestinal inflammation by treatment with probiotics including L. johnsonii can alleviate anxiety"
Link between intestinal bacteria, depression found (2015): https://www.sciencedaily.com/releases/2015/07/150728110734.htm
FMT transfer of depression-like behavior; this study demonstrates that dysbiosis of the gut microbiome may have a causal role in the development of depressive-like behaviors (2016): http://www.nature.com/mp/journal/vaop/ncurrent/full/mp201644a.html
Effects of intestinal microbiota on anxiety-like behavior (2011): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181531/
Dementia:
Review, 2018: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review https://www.dovepress.com/gut-microbiota-cognitive-frailty-and-dementia-in-older-individuals-a-s-peer-reviewed-fulltext-article-CIA "Gut microbiota modulation of cognitive function represents a promising area of research for identifying novel preventive and treatment strategies against dementia"
Herpes virus infection may increase likelihood of dementia (2018): https://www.medicalnewsbulletin.com/herpes-virus-infection-increase-dementia - Herpes Viruses and Senile Dementia: First Population Evidence for a Causal Link (2018): https://doi.org/10.3233/JAD-180266
Gastrointestinal tract microbiota are directly linked to dementia pathogenesis through triggering metabolic diseases and low-grade inflammation progress (2016) https://link.springer.com/article/10.1007%2Fs13238-016-0338-6
Multiple sclerosis (MS):
Review, 2018: The Gut Microbiome and Multiple Sclerosis - "We propose considering the gut microbiome as the major environmental risk factor for CNS demyelinating disease" http://perspectivesinmedicine.cshlp.org/content/early/2018/01/08/cshperspect.a029017
Review, 2017: Gut microbiome in multiple sclerosis: The players involved and the roles they play https://doi.org/10.1080/19490976.2017.1349041
A new study reports T cells are activated in the intestines and migrate to the brain, causing an inflammatory cascade that may lead to multiple sclerosis. Researchers say the gut microbiome may play a more significant role in the development and progression of MS than previously believed. (Oct 2018) https://neurosciencenews.com/multiple-sclerosis-gut-flora-10003/
Researchers at the University of Toronto and UC San Francisco have discovered that the intestine is the source of immune cells that reduce brain inflammation in people with multiple sclerosis (MS) https://www.ucsf.edu/news/2018/12/412941/gut-immune-cells-cut-inflammation-multiple-sclerosis. Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10 (2019): https://doi.org/10.1016/j.cell.2018.11.035
Researchers Uncover Gut Bacteria's Potential Role In Multiple Sclerosis. "We essentially discovered a remote control by which the gut flora can control what is going on at a distant site in the body, in this case the central nervous system" (2018) /r/HumanMicrobiome/comments/8k09k3
Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria (2018): https://doi.org/10.1128/mSystems.00083-18
The makeup of the microbial world in the gut is increasingly recognized as a potential link to the development of the debilitating neurological disease multiple sclerosis. (2016) http://www.labnews.co.uk/features/head-gut-12-12-2016/
Gut bacteria at a young age can contribute to multiple sclerosis disease onset and progression (2017): https://www.sciencedaily.com/releases/2017/11/171117115446.htm
Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models http://www.pnas.org/content/early/2017/09/05/1711235114
Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice (2017) http://www.pnas.org/content/early/2017/09/05/1711233114
Human gut microbe may lead to treatment for multiple sclerosis. Research team tested gut microbial samples from patients on a mouse model of MS. Of three bacterial strains, they discovered that one microbe, Prevotella histicola, effectively suppressed immune disease in the preclinical model of MS. (2017) https://www.eurekalert.org/pub_releases/2017-08/mc-hgm080417.php
High frequency of intestinal TH17 cells correlates with microbiota alterations and disease activity in multiple sclerosis. Our data demonstrate that brain autoimmunity is associated with specific microbiota modifications and excessive TH17 cell expansion in the human intestine. http://advances.sciencemag.org/content/3/7/e1700492
Hidden herpes virus may play key role in MS, other brain disorders. The ubiquitous human herpesvirus 6 may play a critical role in impeding the brain's ability to repair itself in diseases like multiple sclerosis. (2017) https://www.sciencedaily.com/releases/2017/07/170710122959.htm
Fecal microbiota transplantation associated with 10 years of stability in a patient with SPMS (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882466/
Parkinsons:
Parkinsons disease and bacteriophages as its overlooked contributors (2018): https://www.nature.com/articles/s41598-018-29173-4
Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: Gut microbiota, glial reaction and TLR4/TNF-a signaling pathway (2018): https://www.sciencedirect.com/science/article/pii/S0889159118300175
A specific gut bacterium directly induces PD symptoms and dopaminergic neuronal damage in the mouse brain (2018): https://www.nature.com/articles/s41598-018-19646-x
Gut microbiota are related to Parkinson's disease and clinical phenotype: http://www.ncbi.nlm.nih.gov/pubmed/25476529 - http://www.prd-journal.com/article/S1353-8020(16)30323-6/abstract
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease (2016): https://archive.is/WaXjI || Good article coverage: https://scienceofparkinsons.com/2016/12/03/gut-reaction-to-parkinsons-disease/
Review, 2017: Microbes Tickling Your Tummy: the Importance of the Gut-Brain Axis in Parkinson’s Disease https://link.springer.com/article/10.1007%2Fs40473-017-0129-2
Review, 2018: Stomaching the Possibility of a Pathogenic Role for Helicobacter pylori in Parkinson’s Disease http://dx.doi.org/10.3233/JPD-181327
Review, 2018: Can the gut be the missing piece in uncovering PD pathogenesis? https://doi.org/10.1016/j.parkreldis.2018.11.014
PTSD:
PTSD could be prevented with gut microbes (2016): http://www.medicalnewstoday.com/articles/309600.php
Role of gut microbiome in posttraumatic stress disorder. The bacteria in your gut could hold clues to whether or not you will develop posttraumatic stress disorder (PTSD) after experiencing a traumatic event (2017): https://www.sciencedaily.com/releases/2017/10/171025103140.htm
Schizophrenia and bipolar disorder:
Review, 2018: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder: http://www.journalofpsychiatricresearch.com/article/S0022-3956(17)31016-6/abstract
Review, 2017: The microbiome, immunity, and schizophrenia and bipolar disorder https://www.sciencedirect.com/science/article/pii/S0889159116305578
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia (2018): https://www.nature.com/articles/s41398-018-0107-9
Schizophrenia Linked with Abnormal Immune Response to Epstein-Barr Virus (2019): https://www.hopkinsmedicine.org/news/newsroom/news-releases/schizophrenia-linked-with-abnormal-immune-response-to-epstein-barr-virus
He Got Schizophrenia. He Got Cancer. And Then He Got Cured. https://www.nytimes.com/2018/09/29/opinion/sunday/schizophrenia-psychiatric-disorders-immune-system.html "man with leukemia received a bone-marrow transplant from a schizophrenic brother" https://archive.fo/oXUjP#selection-1959.1-1977.1
Genetics:
https://old.reddit.com/s/HumanMicrobiome/wiki/genetics
Maternity:
/s/HumanMicrobiome/wiki/maternity
Mechanisms:
Mechanisms whereby the gut microbiome impacts, regulates, & interacts with the entire body:
Gut microbes are responsible for: Synthesis of vitamins, absorption of minerals, production of epithelial nutrients such as SCFAs, degradation of food components, stimulation of immune system, production of digestive & protective enzymes, prevention of colonization by opportunistic & pathogenic microbes, and more. https://link.springer.com/article/10.1007%2Fs00394-017-1445-8 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577372/ - https://www.ncbi.nlm.nih.gov/pubmed/28984235
Humans have evolved enzymes, receptors, and transporters for the compounds produced by our microbial communities so that the microbiome functions essentially as an endocrine organ: http://www.nyas.org/Publications/EBriefings/Detail.aspx?cid=d7b822c5-4688-4795-9d00-0b11a9719534
Review, 2018: Gut Microbiota and the Neuroendocrine System: https://link.springer.com/article/10.1007%2Fs13311-017-0600-5 - "the gut microbiota is the body’s major neuroendocrine system that controls various body processes in response to stress, the hypothalamic–pituitary–adrenal (HPA) axis"
In addition to secreting neuropeptides, enteroendocrine cells rapidly convey information about nutrients in the gut by releasing neurotransmitters (glutamate) to excite vagal and spinal sensory neurons. (2018): https://doi.org/10.1126/science.aau9973 "The finding that gut enteroendocrine cells form glutamatergic synapses identifies a first relay in the neural circuit through which the brain detects gastrointestinal contents, such as nutrients and microbes, to control satiety, metabolism, and digestion."
Influence the activation of peripheral immune cells, which regulate responses to neuroinflammation, brain injury, autoimmunity and neurogenesis: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4476.html
Amyloid produced by commensal bacteria may cause changes in protein folding and neuroinflammation in the central nervous system through the autonomic nervous system (particularly the vagus nerve), the trigeminal nerve in the mouth and nasopharynx, and the gut (including mouth, esophagus, stomach and intestines), as well as via the olfactory receptors in the roof of the nose. https://www.sciencedaily.com/releases/2017/12/171222090323.htm
Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve: http://www.sciencedirect.com/science/article/pii/S0304394017308261
The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis (2018): https://www.frontiersin.org/articles/10.3389/fnins.2018.00049/full
Gut microbes can communicate with the brain through a variety of routes, including the vagus nerve, short-chain fatty acids (SCFAs), cytokines, and tryptophan: http://www.sciencedirect.com/science/article/pii/S0889855316300826
Researchers Uncover Gut Bacteria's Potential Role In Multiple Sclerosis. "We essentially discovered a remote control by which the gut flora can control what is going on at a distant site in the body, in this case the central nervous system" (2018) /r/HumanMicrobiome/comments/8k09k3
Gastrointestinal neuromuscular apparatus: https://archive.is/wPHGF
TLR2 may act in intestinal pathophysiology, not only by its inherent innate immune role, but also by regulating the intestinal serotoninergic system http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169303 - https://www.eurekalert.org/pub_releases/2016-12/uoe-gma122316.php
Bacterial Signaling to the Nervous System via Toxins and Metabolites: http://www.sciencedirect.com/science/article/pii/S0022283617300141
Immunoregulatory circuits engaging epithelial and mesenchymal cells in the intestine, airways, and skin. Immune communications with hematopoietic cells and the microbiota orchestrate local immune homeostasis and inflammation: http://www.sciencedirect.com/science/article/pii/S0092867416316506
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota (2017): http://msystems.asm.org/content/2/5/e00107-17
Bidirectional signaling between the brain and the gastrointestinal tract is regulated at neural, hormonal, and immunological levels. https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-016-2146-2
Quorum sensing & electrical signaling: https://www.theatlantic.com/science/archive/2017/01/bacteria-electrical-pulse/512825/ - https://medicalxpress.com/news/2018-06-food-affects-biochemical-gut.html
Extracellular Vesicles: https://synapse.koreamed.org/DOIx.php?id=10.4168/aair.2017.9.2.101
Gut's microbial community shown to influence host gene expression; epigenomic regulation: https://www.eurekalert.org/pub_releases/2016-11/uow-gmc111816.php - http://www.sciencedirect.com/science/article/pii/S0952791516301558 - https://doi.org/10.1101/210294 - https://doi.org/10.1101/210294
Gut microbiota has a widespread and modifiable effect on host gene regulation (2018): https://doi.org/10.1101/210294
Redox signaling mediated by the gut microbiota. Redox imbalances have been correlated with every single disease. https://archive.is/yrhJM - https://www.nature.com/articles/s41575-018-0079-5
microRNAs (miRNAs) act at the epicenter of the signaling networks regulating intestinal homeostasis: http://onlinelibrary.wiley.com/doi/10.1002/bies.201600200/full - https://doi.org/10.1053/j.gastro.2017.11.076
Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4: http://www.jbc.org/content/early/2017/07/31/jbc.M117.788596
Review, 2017: MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome https://www.frontiersin.org/articles/10.3389/fmicb.2017.01896/full
Microbiota may control intestinal epithelial stem cell (IESC) proliferation in part through microRNAs (miRNAs). http://www.jbc.org/cgi/doi/10.1074/jbc.M116.770099 | review: http://journal.frontiersin.org/article/10.3389/fimmu.2017.00599/full
Gut microbes seem to influence miRNAs in the amygdala and the prefrontal cortex: https://www.eurekalert.org/pub_releases/2017-08/bc-rsn082217.php
Eukaryotic/host miRNAs play a role in the replication/propagation of viruses, affect life-cycles & infection pathways: http://journal.frontiersin.org/article/10.3389/fmicb.2017.00824/full More virus-host genome interactions: https://doi.org/10.1101/142604
Bacterium orchestrates gastric epithelial stem cells and gland homeostasis: https://medicalxpress.com/news/2017-08-stem-cells-link-bacteria-cancer.html
Maintain oxygen balance & homeostasis in the gut via peroxisome proliferator-activated receptor-? (PPAR?) : https://sci-hub.tw/http://www.nature.com/nrmicro/journal/vaop/ncurrent/full/nrmicro.2017.112.html
Nutrient poor environment causes bacteria to adapt, this causes host to store more fat. Direct communication with mitochondria: https://www.sciencedaily.com/releases/2017/04/170424110844.htm
How dietary fiber (DF) intake elicits a wide range of physiologic effects, not just locally in the gut, but systemically. http://advances.nutrition.org/content/7/6/1111.long
Most of effects are mediated through metabolites acting as energy sources, signaling molecules, receptor ligands and substrates for host enzymes. https://doi.org/10.2174/1570161115666170105095834
Enteric nervous system modulates gut microbiota community: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000689
Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer (2017): https://www.news-medical.net/news/20171107/Researchers-identify-mechanisms-through-which-H-pylori-bacteria-cause-gastric-cancer.aspx
Microbial metabolite contributes to the accumulation of lipids in the liver and hence to nonalcoholic steatohepatitis (2018): https://www.nature.com/articles/s41591-018-0126-3
A single genetic change in gut bacteria alters host metabolism via bacterial enzyme impacting bile metabolism (2018): https://www.eurekalert.org/pub_releases/2018-07/e-asg071718.php
Accelerate Wound Healing via multiple mechanisms [1][2].
Misc:
Reddit search results (q&a's with researchers, etc.): https://old.reddit.com/search?q=microbiome&feature=legacy_search
Google drive study archive – "substantial emerging literature on intestinal overgrowth, gut barrier permeability, endotoxemia, systemic inflammation, and chronic disease": https://archive.is/hdxjn
Fecal Microbiota Transplants (FMT):
Obesity & diet:
Gut flora manipulate (through the vagus nerve) their host's eating patterns & cravings, behavior & mood, taste receptors, and more: https://motherboard.vice.com/en_us/article/ezvbjp/gut-bacteria-controls-your-brain
Recent data show a link between the diversity and richness of gut microbiota and the way we store fat, how we regulate digestion hormones and blood glucose levels, and even what types of food we prefer: /r/HumanMicrobiome/comments/6to7kb
Review, 2012: Impact of the Gut Microbiota on the Development of Obesity: Current Concepts: http://www.nature.com/ajgsup/journal/v1/n1/full/ajgsup20125a.html
Review, 2016: Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045147/
Review, 2017: Fecal microbiota transplantation in metabolic syndrome: History, present and future http://www.tandfonline.com/doi/full/10.1080/19490976.2017.1293224
Review, 2018: Gut Microbes and Health: A Focus on the Mechanisms Linking Microbes, Obesity, and Related Disorders: https://onlinelibrary.wiley.com/doi/abs/10.1002/oby.22175
Review, 2018: Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives: https://link.springer.com/article/10.1007%2Fs13238-018-0546-3
Review, 2018: Importance of gut microbiota in obesity https://www.nature.com/articles/s41430-018-0306-8 "the increase in fat mass is not only due to a more efficient harvest of energy, but also the microbiota participates in changes in endotoxemia, bowel permeability, insulin resistance, hormonal environment, expression of genes regulating lipogenesis, interaction with bile acids, as well as changes in the proportion of brown adipose tissue, and effects associated with the use of drugs such as metformin"
Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to High Fructose Consumption in Mice (2018): https://doi.org/10.1101/439786
A single genetic change in gut bacteria alters host metabolism via microbial enzymes impacting bile metabolism (2018): https://www.eurekalert.org/pub_releases/2018-07/e-asg071718.php
Adenovirus 36 and Obesity: An Overview (2015): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517116/
The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis (2018): https://doi.org/10.1016/j.chom.2018.08.009
Host genotype affects the abundance of taxa associated with metabolic disease. Gut microbiota affects susceptibility to diet-induced metabolic disease. The gut microbiome modulates insulin secretion: http://www.cell.com/cell-reports/abstract/S2211-1247(17)30119-5
Long term but not short term exposure to obesity related microbiota promotes host insulin resistance (2018): https://www.nature.com/articles/s41467-018-07146-5
Study Links BMI, Lipid Levels to Gut Microbes. http://www.hcplive.com/medical-news/new-study-links-bmi-lipid-levels-to-gut-microbes || Including fungal mycobiota: http://www.nature.com/articles/srep14600
Fat and thin people have different gut bacteria: https://doi.org/10.1002/oby.22320 - https://www.sciencedaily.com/releases/2016/09/160920130825.htm - https://www.sciencedaily.com/releases/2016/09/160926221634.htm
Heritable components of the human fecal microbiome are associated with visceral fat: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1052-7 | Maternal prepregnancy obesity may imprint a selective gut microbial composition during late infancy with distinct functional performances: https://link.springer.com/article/10.1007/s13105-017-0577-x
Gut bacteria can help to predict how the body will respond to fatty foods. Chemical signatures from gut bacteria which show up in urine can be used to predict how the body will respond to a 'junk' diet. https://www.eurekalert.org/pub_releases/2017-07/icl-gbc070417.php
Doctors call for fecal transplant regulation after seeing unexpected results (obesity transfer in people): http://stirling-westrup-tt.blogspot.com/2015/06/tt-ns-3024-doctors-call-for-faecal.html - http://www.webmd.com/digestive-disorders/news/20151209/diy-fecal-transplant#4 - http://ofid.oxfordjournals.org/content/2/1/ofv004.full
Transfer of Obesity via the Gut Microbiome is Mediated Specifically through Suppression of Non-Aerobic Resting Metabolism: http://www.fasebj.org/content/29/1_Supplement/857.2.short || They found it wasn't just the bacteria that could produce this effect. Transferring just the bacteriophage was sufficient to reduce resting metabolic rate and cause weight gain in control mice: https://www.sciencedaily.com/releases/2015/12/151214130811.htm
When researchers in China took a strain of E. cloacae (B29) from the gut of a volunteer who weighed in at 385 pounds and transplanted it into germ-free mice, the rodents themselves then became obese compared to similar mice fed an identical diet, but without the E. cloacae: http://www.ubiomeblog.com/the-surprising-connection-between-you-and-a-giant-panda/ - http://www.nature.com/ismej/journal/v7/n4/full/ismej2012153a.html
Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children: https://archive.is/zRg8p
Nutrient poor environment causes bacteria to adapt, this causes host to store more fat. Direct communication with mitochondria: https://www.sciencedaily.com/releases/2017/04/170424110844.htm
Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity http://www.pnas.org/content/110/22/9066.short
A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice: http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.4236.html
An intestinal microbiota-farnesoid X receptor axis modulates metabolic disease. Mice lacking expression of FXR in the intestine were resistant to (High Fat Diet)HFD-induced obesity, insulin resistance and NAFLD thus confirming that intestinal FXR is involved in the potentiation of metabolic disease: http://www.gastrojournal.org/article/S0016-5085(16)35038-7/pdf Gut microbiota, FXR, and bile acids as regulators of host metabolism: http://diabetes.diabetesjournals.org/content/66/3/571.long
Dual-specificity phosphatase 6 deficiency regulates gut microbiome and transcriptome response against diet-induced obesity in mice: http://www.nature.com/articles/nmicrobiol2016220
Short Chain Fatty Acids Prevent High-fat-diet-induced Obesity in Mice by Regulating G Protein-coupled Receptors and Gut Microbiota: http://www.nature.com/articles/srep37589
Dietary fat and gut microbiota interactions determine diet-induced obesity in mice (& difference between animal fat & vegetable fat) http://www.molmetab.com/article/S2212-8778(16)30189-2/pdf
TED talk by microbiome researcher (obesity part around 11:30): https://www.youtube.com/watch?v=i-icXZ2tMRM
Freeze-dried poop pills being tested for obesity treatment: http://arstechnica.com/science/2016/01/freeze-dried-poop-pills-being-tested-for-obesity-treatment/
The gut microbiota affects calorie harvest and energy homeostasis. Germ-free mice have 40% less total body fat than conventional mice although they ingest 29% more calories than their conventionally raised littermates. Fecal microbiota transplanted from conventionally raised mice to germ-free mice triggered a 57 % increase in the amount of body fat and a dramatic increase in hepatic triglyceride levels and insulin resistance without modifying the amount of food consumed: http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0303-2 || Germ-free lab mice also suffer various problems: https://archive.is/1Rxak - https://www.clinicalkey.com/#!/content/playContent/1-s2.0-S0306452216305127
Children who take antibiotics gain weight faster: https://archive.is/pqE1t - http://www.jpeds.com/article/S0022-3476(16)30375-4/fulltext - http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0245-y || Also seen in feed animals (along with pro & pre biotics): http://www.sciencedirect.com/science/article/pii/S0882401015301881
Effect of diet soda on gut bacteria: http://www.npr.org/blogs/thesalt/2014/09/17/349270927/diet-soda-may-alter-our-gut-microbes-and-the-risk-of-diabetes – http://www.prevention.com/health/diabetes/artificial-sweeteners-diet-soda-affect-gut-bacteria-and-weight-gain
Artificial sweeteners induce glucose intolerance by altering the gut microbiota: http://www.nature.com/nature/journal/v514/n7521/full/nature13793.html | And block enzyme activity: https://www.eurekalert.org/pub_releases/2016-11/mgh-amp112216.php Artificial Sweeteners May Change Our Gut Bacteria in Dangerous Ways: https://www.scientificamerican.com/article/artificial-sweeteners-may-change-our-gut-bacteria-in-dangerous-ways/
Changes in the microbiome may contribute to cognitive changes associated with eating a Western diet: https://ir.library.oregonstate.edu/xmlui/bitstream/handle/1957/55795/MagnussonKathyBiomedicalSciencesRelationshipsBetweenDietRelatedChanges.pdf
Effects of Gut Microbes on Nutrient Absorption and Energy Regulation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601187/
Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates: http://www.cell.com/cell-metabolism/abstract/S1550-4131%2814%2900311-8
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice: http://stm.sciencemag.org/content/1/6/6ra14.long
Diet rapidly and reproducibly alters the human gut microbiome: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957428/
Review, 2017: Influence of diet on the gut microbiome and implications for human health https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385025/
Resistant starch alters intestinal microbiota: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146406 - https://carcin.oxfordjournals.org/content/early/2016/02/18/carcin.bgw019.abstract?sid=c46f200d-7651-4b92-acec-92f27ffa18dc
Fast food fever: reviewing the impacts of the Western diet on immunity. Dietary impact on the gut microbiome and the mechanisms by which our poor dietary choices are encoded into our gut, our genes, and are passed to our offspring: http://www.ncbi.nlm.nih.gov/pubmed/24939238
Diet-induced extinctions in the gut microbiota compound over generations (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850918/
Origins:
/s/HumanMicrobiome/wiki/origins
Other studies & articles:
Effect of the Gut Microbiota on Obesity, gut permeability, inflammation, immune system, metabolism, probiotics, diet, FMT: an Update (2015) http://www.besjournal.com/Articles/Archive/2015/No11/201512/t20151218_123660.html
Therapeutic opportunities in the human microbiome (2012): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287364/
Gut Microbes Can Evolve From Foe to Friend—And Do It Fast: http://phenomena.nationalgeographic.com/2016/03/28/microbes-can-quickly-evolve-to-protect-hosts-from-disease/
Allergy:
Review, 2018: Microbiome and Allergic Diseases https://www.frontiersin.org/articles/10.3389/fimmu.2018.01584/full "Recent research points to a central role of the microbiome"
Review, 2018: Microbiota and Food Allergy https://doi.org/10.1007/s12016-018-8723-y "evidence suggests that the increasing prevalence of food allergies is associated with compositional and functional changes in our gut microbiota; mechanistic details not fully understood" | Another: https://doi.org/10.1016/j.anai.2018.12.012
Gut Microbes from Healthy Infants Block Milk Allergy Development in Mice. https://www.niaid.nih.gov/news-events/gut-microbes-healthy-infants-block-milk-allergy-development-mice. Healthy infants harbor intestinal bacteria that protect against food allergy (2019): https://doi.org/10.1038/s41591-018-0324-z
Perinatal antibiotic exposure alters composition of murine gut microbiota and may influence later responses to peanut antigen (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211427/ "Our data suggest that early antibiotic exposure promotes a shift in the gut microbiota community that may in turn, influence how mice later respond to a TNF-a + antigen challenge"
Commensal bacteria protect against food allergen sensitization (2014): https://doi.org/10.1073/pnas.1412008111 "We show here that sensitization to a food allergen is increased in mice that have been treated with antibiotics or are devoid of a commensal microbiota"
Allergies/immune response patterns are shaped by microbial exposures and diet in the pregnant mother and during the infant’s first years: https://jamanetwork.com/journals/jamapediatrics/article-abstract/2481804 (more in the pregnancy & birth listing: /s/HumanMicrobiome/wiki/maternity)
American adults with allergies have low gut microbe diversity: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739432/ "Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project (2016)"
A metagenome-wide association study of gut microbiota in asthma in UK adults (2018): https://doi.org/10.1186/s12866-018-1257-x "The microbiota of the individuals with asthma consisted of fewer microbial entities than the microbiota of healthy individuals. The adult human gut microbiome of asthma patients is clearly different from healthy controls."
Newborn Gut Microbiome Predicts Later Allergy and Asthma: https://scienceblog.com/487931/newborn-gut-microbiome-predicts-later-allergy-asthma-study-finds/
Causality between certain gut microbiota and the development of allergic asthma has been shown in experiments conducted in neonatal mice: https://www.sciencedirect.com/science/article/pii/S0091674917303172
A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model (2016): http://www.sciencedirect.com/science/article/pii/S152166161630300X
Relationship between a viral detection system (MAVS), the composition of the gut microbiota, and the development of skin allergies (2018): https://www.sciencedaily.com/releases/2018/09/180925110017.htm after FMT from allergic mice the recipients "developed severe allergic reactions, showing that the transplanted gut bacteria were responsible"
Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells (2018): https://doi.org/10.1016/j.jaci.2018.07.046
Autoimmunity:
Re-framing the Theory of Autoimmunity in the Era of the Microbiome: Persistent Pathogens, Autoantibodies, and Molecular Mimicry (2018): http://www.discoverymedicine.com/Amy-D-Proal/2018/06/autoimmunity-in-era-of-microbiome-persistent-pathogens-autoantibodies-molecular-mimicry/ - The theory of autoimmunity was developed at a time when the human body was regarded as largely sterile. Antibodies in patients with chronic inflammatory disease could consequently not be tied to persistent human pathogens. The concept of the "autoantibody" was created to reconcile this phenomenon. This calls for a paradigm shift in autoimmune disease treatment.
Review, 2018: Antibiotics and autoimmune and allergy diseases: Causative factor or treatment? https://www.sciencedirect.com/science/article/pii/S1567576918304752 "Antibiotics use in children promotes the development of allergic disorders, whereas antibiotics use in adults seems to ameliorate inflammatory responses and reduce the severity of autoimmune diseases"
The role of gut microbiota in lupus: what we know in 2018? https://doi.org/10.1080/1744666X.2018.1519395 "Current data demonstrates that, depending on the pattern of intestinal microorganisms or the presence of specific bacteria, different responses related to lupus physiology can be triggered. Fecal microbiota transplantation, live biotherapeutics, or dietary interventions targeting the microbiota will likely become a treatment for SLE."
Translocation of a gut pathobiont drives autoimmunity in mice and humans (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959731/
New Link Between Autoimmune Diseases and a Gut Bacterium (b. fragilis). Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis : a potential link with autoimmune disease (2018): http://dx.doi.org/10.1111/cei.13195 - https://medicalxpress.com/news/2018-10-ground-breaking-discovery-link-autoimmune-diseases.html
Cardiovascular:
Review, 2018: Role of gut microbiota in chronic low-grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies https://doi.org/10.1111/obr.12750
Review, 2018: Effects of products designed to modulate the gut microbiota on hyperlipidaemia https://doi.org/10.1007/s00394-018-1821-z "Products designed to modulate the gut microbiota results in changes of the plasma lipid concentrations and these changes may protect against cardiovascular disease"
Multiple reviews connecting cardiovascular disease to the gut microbiome: /r/HumanMicrobiome/comments/6t4vou
Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry (2018): https://www.biorxiv.org/content/early/2018/08/17/394726
Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome (2018): https://doi.org/10.1038/s41588-018-0224-7 "This study provides important evidence for a joint genetic and microbial effect in cardiovascular disease and provides directions for future applications in personalized medicine"
Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential (2018): https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.118.313142
The gut microbiome in atherosclerotic cardiovascular disease (2017): https://www.nature.com/articles/s41467-017-00900-1
Gut Microbiota–Dependent Trimethylamine N-Oxide (TMAO) Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes (2018): https://doi.org/10.1161/ATVBAHA.118.311023
Gut microbiome can influence common dietary compound (TMAO) linked to heart disease: http://www.news-medical.net/news/20160811/Gut-microbiome-can-influence-common-dietary-compound-linked-to-heart-disease.aspx | Targeting the gut microbiome to fight heart disease - Resveratrol reduces levels of TMAO and TMA: https://www.eurekalert.org/pub_releases/2016-04/asfm-ttg033116.php
Tomorrow’s Heart Drugs Might Target Gut Microbes. Scientists can stop gut bacteria in mice from making a chemical that causes arterial disease (2015): http://www.theatlantic.com/science/archive/2015/12/tomorrows-heart-drugs-might-target-gut-microbes/420900
Bacterial Fats, not Butter, May Be to Blame for Heart Disease (2017): /r/HumanMicrobiome/comments/7amw18
Bacteria Help Regulate Blood Pressure: Kidneys sniff out signals from gut bacteria for cues to moderate blood pressure after meals. https://www.quantamagazine.org/how-bacteria-help-regulate-blood-pressure-20171130/
Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants (2016): http://circres.ahajournals.org/content/119/8/956
Atherosclerosis:
Commensal Microbe-specific Activation of B2 Cell Subsets Contributes to Atherosclerosis Development Independently of Lipid Metabolism: http://www.sciencedirect.com/science/article/pii/S2352396416304911
An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis (2018): https://doi.org/10.1016/j.immuni.2018.09.011
Bacterial butyrate prevents atherosclerosis by maintaining gut barrier function in mice. Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model (Nov 2018) https://www.gutmicrobiotaforhealth.com/en/bacterial-butyrate-prevents-atherosclerosis-by-maintaining-gut-barrier-function-in-mice/
Stroke and transient ischemic attack:
Review, 2016: The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke: https://link.springer.com/article/10.1007/s13311-016-0475-x - "Transplantation of balanced microbiota after cerebral ischemia improved stroke outcome"
Commensal microbiota affects ischemic stroke outcome by regulating intestinal ?d T cells (2016): https://www.nature.com/articles/nm.4068 "antibiotic-induced alterations in the intestinal flora reduce ischemic brain injury in mice, an effect transmissible by fecal transplants"
Microbiota Dysbiosis Controls the Neuroinflammatory Response after Stroke (2016): http://www.jneurosci.org/content/36/28/7428.long
Dysbiosis of Gut Microbiota With Reduced Trimethylamine-N-Oxide Level in Patients With Large-Artery Atherosclerotic Stroke or Transient Ischemic Attack: http://jaha.ahajournals.org/content/4/11/e002699
Heart failure:
Review, 2018: The gut microbiome and heart failure https://journals.lww.com/co-cardiology/Abstract/publishahead/The_gut_microbiome_and_heart_failure.99129.aspx "exact mechanisms of action remain unclear; investigating the gut microbiome as a potential strategy for clinical intervention is highly warranted"
Review, 2018: Dietary metabolism, the gut microbiome, and heart failure https://www.nature.com/articles/s41569-018-0108-7
Review, 2017: Targeting the Microbiome in Heart Failure: https://link.springer.com/article/10.1007%2Fs11936-017-0528-4
Pathogenic Gut Flora Tied to Heart-Failure Severity (2016): http://www.heartfailure.onlinejacc.org/content/4/3/220 - http://www.medscape.com/viewarticle/856123
Heart failure is associated with depletion of core intestinal microbiota (2017): http://onlinelibrary.wiley.com/doi/10.1002/ehf2.12155/full
Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients (2018): https://www.nature.com/articles/s41598-017-18756-2
Heart failure: Destroying gut bacteria could improve outcomes. Gut microbiota depletion preserves heart function, suppresses cardiac fibrosis and hypertrophy in a non-ischemic heart failure mouse model (2018): https://www.medicalnewstoday.com/articles/321584.php - https://www.fasebj.org/doi/10.1096/fasebj.2018.32.1_supplement.287.3
Cholesterol:
Bacteria pill is 'better than statins' in the war on cholesterol, say researchers. Trials of the new treatment showed cholesterol falling 37% in patients who were suffering from harmfully high levels in their system: http://www.mirror.co.uk/science/bacteria-pill-better-statins-war-7841790
A link has been discovered between bacteria in the gut and body weight, triglyceride and good cholesterol levels. Researchers identified 34 specific digestive tract microorganism species that influence weight and lipid metabolism: https://www.sciencedaily.com/releases/2015/09/150910164220.htm
Blood pressure:
Review, 2017: "In this review, we compile the recent findings and hypotheses describing the interplay between the microbiome and blood pressure": http://journal.frontiersin.org/article/10.3389/fped.2017.00138/full
Cancer:
Review, 2018: The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It. "To date, microbes can be linked to almost every cancer, including colon, pancreatic, gastric, and even prostate." http://www.mdpi.com/2072-6694/10/3/83/htm
Review, 2017: The human microbiome and cancer: http://cancerpreventionresearch.aacrjournals.org/content/10/4/226 - http://sci-hub.tw/10.1158/1940-6207.CAPR-16-0249
Review, 2017: Research now suggests that the microbiota — commensal microorganisms including bacteria, fungi, and viruses that inhabit an organism — plays an important role in carcinogenesis, cancer progression, and treatment response: http://www.cancertherapyadvisor.com/fact-sheets/microbiota-cancer-oncology-fact-sheet/article/733468/
Review, 2016: Microbiota dysbiosis: a new piece in the understanding of the carcinogenesis puzzle: http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.000371
Review, 2013: The microbiome and cancer: http://www.nature.com/nrc/journal/v13/n11/abs/nrc3610.html
Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2965-y
Breast Microbiome Changes May Alter Breast Cancer Risks: http://www.genengnews.com/gen-news-highlights/breast-microbiome-changes-may-alter-breast-cancer-risks/81253051/
Microbiome Makeup Determines Whether Rats Get Colon Cancer: https://www.alnmag.com/news/2016/07/microbiome-makeup-determines-whether-rats-get-colon-cancer
Gut bacteria could help prevent cancer. New research offers evidence that anti-inflammatory 'health beneficial' gut bacteria can slow or stop the development of some types of cancer: https://www.sciencedaily.com/releases/2016/04/160413151108.htm
Microbes Meet Cancer. Understanding cancer’s relationship with the human microbiome could transform immune-modulating therapies: http://www.the-scientist.com/?articles.view/articleNo/45616/title/Microbes-Meet-Cancer/
What gut bacteria can teach us about cancer treatment. Studies probe link between gut bacteria and treatment effectiveness: http://www.mnn.com/health/fitness-well-being/blogs/what-gut-bacteria-can-teach-us-about-cancer-treatment
How Gut Bacteria Are Shaking Up Cancer Research: https://web.archive.org/web/20170127012130/https://www.bloomberg.com/news/articles/2016-03-14/how-gut-bacteria-are-shaking-up-cancer-research
Disparities in Gut Microbiome Could Lead to Biomarkers for Estrogen-driven Breast Cancer: http://www.oncologynurseadvisor.com/breast-cancer/effect-of-estrobolome-on-breast-cancer-evaluated/article/494462/
Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota (2015): https://doi.org/10.1126/science.aad1329
More: /s/HumanMicrobiome/wiki/cancer
CFS/ME:
Review, 2018: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity https://doi.org/10.3389/fped.2018.00373
Review, 2018: Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? This article provides a comprehensive review of the current evidence supporting microbiome alterations in ME/CFS patients. http://www.clinsci.org/content/132/5/523
Review, 2016: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? http://www.mdpi.com/2077-0383/5/6/55
Review, 2009: Leaky gut in chronic fatigue syndrome: A review https://www.researchgate.net/publication/280641339_R_E_V_I_E_W_Leaky_gut_in_chronic_fatigue_syndrome_A_review - "The purpose of this paper is to review the evidence that an increased translocation of gram negative bacteria is another inflammatory pathway that is involved in CFS"
Insights from metabolites get us closer to a test for chronic fatigue syndrome. "Combining this data with data from an earlier microbiome study, the researchers now report they can predict whether or not someone has the disorder with a confidence of 84 percent" https://medicalxpress.com/news/2018-07-insights-metabolites-closer-chronic-fatigue.html | Dorottya Nagy-Szakal et al, Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics, Scientific Reports (2018). DOI: http://dx.doi.org/10.1038/s41598-018-28477-9
Chronic fatigue syndrome is in your gut, not your head. Cornell identifies biological markers (2016): https://www.sciencedaily.com/releases/2016/06/160627160939.htm - http://www.genengnews.com/gen-news-highlights/chronic-fatigue-syndrome-it-s-all-in-your-gut/81252887/
The gut microbiome in Myalgic Encephalomyelitis (page 10, Cornell, 2017): http://www.biochemistry.org/Portals/0/Biochemist/Apr17-compressedv2.pdf
Increased D-Lactic bacteria in CFS patients: http://iv.iiarjournals.org/content/23/4/621.long
A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Differ in Physiological Parameters and Gut Microbiome Composition (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5058431/
2017 Columbia University study confirms "Chronic Fatigue Syndrome Associated with Abnormal Gut Microbes": https://archive.is/FkrLE
Thomas J Borody's 2012 CFS FMT study with 70% initial success rate: Bacteriotherapy in Chronic Fatigue Syndrome (CFS): A Retrospective Review http://www.cdd.com.au/pdf/publications/All%20Publications/2012-Bacteriotherapy%20in%20chronic%20fatigue%20syndrome%20(CFS)-%20a%20retrospective%20review.pdf - https://search.informit.com.au/documentSummary;dn=119626231492520;res=IELHEA - Full paper: https://web.archive.org/web/20180831204424/http://www.superbugskill.com/papers/cfscure.pdf
Exercise – induced changes in cerebrospinal fluid miRNAs in Gulf War Illness, Chronic Fatigue Syndrome and sedentary control subjects. Changes in brain chemistry -- observed in levels of miRNAs that turn protein production on or off -- were seen 24 hours after riding a stationary bike for 25 minutes. https://www.nature.com/articles/s41598-017-15383-9 - See the "mechanisms" section for info on gut microbe's influence on miRNAs.
Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) (2015): https://doi.org/10.1371/journal.pone.0145453 "findings suggest a role for an altered gut microbiome and increased bacterial translocation following exercise in ME/CFS patients that may account for the profound post-exertional malaise experienced by ME/CFS patients"
Celiac:
Duodenal Bacteria From Patients With Celiac Disease and Healthy Subjects Distinctly Affect Gluten Breakdown and Immunogenicity: http://www.sciencedirect.com/science/article/pii/S0016508516347138
Bacteria from celiac patients influence gluten’s digestion and its ability to provoke an immune response: http://www.gutmicrobiotaforhealth.com/en/bacteria-celiac-patients-influence-glutens-digestion-ability-provoke-immune-response/
Experimental hookworm infection and gluten microchallenge promote tolerance in celiac disease (2015): https://www.ncbi.nlm.nih.gov/pubmed/25248819 - https://www.iflscience.com/health-and-medicine/parasitic-worms-trialed-treatment-celiac-disease/
C.Diff:
Antibiotics disrupt the beneficial bacteria found in the gut and make patients more likely to get C. difficile: http://www.cavalierdaily.com/article/2016/08/u-va-researchers-make-important-discovery-about-dangerous-bacteria
Diabetes:
/r/diabetes/comments/6qr87q
Hormones:
Review, 2017: Steroids, Stress, and the Gut Microbiome-Brain Axis. "steroids can influence the gut microbiota, and in turn the gut microbiota can influence hormone levels" https://sci-hub.tw/http://onlinelibrary.wiley.com/doi/10.1111/jne.12548/abstract
Oral supplementation with probiotic L. reuteri NCIMB 30242 increases mean circulating 25-hydroxyvitamin D: a post hoc analysis of a randomized controlled trial: http://www.ncbi.nlm.nih.gov/pubmed/23609838
Gut microbes may partner with a protein to help regulate vitamin D (2018): https://news.psu.edu/story/525922/2018/06/28/research/gut-microbes-may-partner-protein-help-regulate-vitamin-d
Male steroid hormones: http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=48671
Researchers found predictive relationships between the fecal microbiota and serotonin and cortisol: /r/HumanMicrobiome/comments/6v8gck
Gut microbiota induce IGF-1 and promote bone formation and growth (in mice). In contrast, antibiotic treatment does opposite: http://www.pnas.org/content/early/2016/11/04/1607235113.abstract
HIV:
Review, 2018: Gut microbiota in diabetes and HIV: Inflammation is the link https://www.ebiomedicine.com/article/S2352-3964(18)30512-7/fulltext
Review, 2016: Microbiome alterations in HIV infection a review: http://onlinelibrary.wiley.com/doi/10.1111/cmi.12588/abstract
Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals (2018): https://www.ebiomedicine.com/article/S2352-3964(18)30111-7/pdf
Bacteria in our gut affects HIV—is there a solution? http://betablog.org/9074-2/
How Gut Microbiota Impacts HIV Disease. A new understanding of the role gut microbiota plays in HIV disease is beginning to emerge, suggesting potential new strategies to manage the infection: http://www.scientificamerican.com/article/how-gut-microbiota-impacts-hiv-disease/
Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals: http://www.sciencedirect.com/science/article/pii/S2352396416301761
Understanding the Gut Microbiome and HIV: http://www.vaxreport.org/vax-april-2016/896-understanding-the-gut-microbiome-and-hiv
Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen: http://bmjopengastro.bmj.com/content/3/1/e000080
Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection (2018): https://doi.org/10.1038/s41385-018-0083-7 "low nadir CD4+ T-cell counts, rather than HIV-1 serostatus per se, predict the presence of gut dysbiosis in HIV-1 infected subjects. Such dysbiosis does not display obvious HIV-specific features; instead, it shares many similarities with other diseases featuring gut inflammation"
IBD:
Review, 2018: The role of fecal microbiota transplantation in inflammatory bowel disease. "Despite high heterogenity in all areas of procedure, overall, this review supports a positive effect of FMT on outcome of IBD and FMT was well tolerated for the majority of patients." https://onlinelibrary.wiley.com/doi/abs/10.1111/1751-2980.12603 | Another 2018 review: Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation https://link.springer.com/article/10.1007/s11908-018-0627-8
Review, 2018: Fecal microbiota transplant – a new frontier in inflammatory bowel disease https://doi.org/10.2147/JIR.S176190 "Clinical trials data are still poor but strongly support a future introduction of FMT in therapy to manage IBD microbiome. More studies are needed to assess the optimal route of administration and the frequency of FMT, the best matched donor for each patient as well as the risks associated with FMT in IBD"
Review, 2017: Gut microbiota in the pathogenesis of inflammatory bowel disease: https://link.springer.com/article/10.1007%2Fs12328-017-0813-5
Review, 2016: The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis: http://www.tandfonline.com/doi/full/10.1080/00365521.2016.1216587
Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and ROR?t+ Regulatory T Cells and Exacerbate Colitis in Mice (2019): https://doi.org/10.1016/j.immuni.2018.12.015
Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease (2018): https://doi.org/10.1080/19490976.2018.1511664 "findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD"
Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells (2017): http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31417-1
Worm infection counters inflammatory bowel disease by drastically changing gut microbiome: https://www.sciencedaily.com/releases/2016/04/160414145513.htm
Breakdown products from microcin B17, a well-known toxin produced by E. coli, seem to trigger gut inflammation that is characteristic of IBD (2018): https://medicalxpress.com/news/2018-05-chance-discovery-links-inflammatory-bowel.html
Crohns:
Multiple fresh fecal microbiota transplants induces and maintains clinical remission in Crohn’s disease complicated with inflammatory mass (2017): https://www.nature.com/articles/s41598-017-04984-z
The fecal microbiota as a biomarker for disease activity in Crohn’s disease (2016): http://www.nature.com/articles/srep35216
A microbial signature for Crohn's disease (2017): http://gut.bmj.com/content/66/5/813
Serologic microbial associated markers can predict Crohn's disease behaviour years before disease diagnosis (2016): http://onlinelibrary.wiley.com/doi/10.1111/apt.13641/abstract
Genetic Variant Newly Linked to Crohn’s Disease Also Associated with Altered Gut Microbiome Composition (2016): http://www.prweb.com/releases/2016/07/prweb13585245.htm
Case Western Reserve-Led International Team Identifies Fungus in Humans for First Time as Key Factor in Crohn’s Disease (2016): http://www.newswise.com/articles/case-western-reserve-led-international-team-identifies-fungus-in-humans-for-first-time-as-key-factor-in-crohn-s-disease
A role for bacterial urease in gut dysbiosis and Crohn’s disease. Bacterial (E. coli) enzyme (urease) reconfigures the entire gut microbiome and worsens immune-mediated colitis: https://www.sciencedaily.com/releases/2017/11/171115144142.htm
Ulcerative Colitis:
Fecal Transplants Effective: http://www.hcplive.com/medical-news/fecal-transplants-effective-for-healing-ulcerative-colitis
Efficacy of fecal microbiota therapy in steroid dependent ulcerative colitis: a real world intention-to-treat analysis (2019): https://doi.org/10.5217/ir.2018.00089
Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis. A Randomized Clinical Trial (2019): https://jamanetwork.com/journals/jama/article-abstract/2720727 "1-week treatment with anaerobically prepared donor FMT compared with autologous FMT resulted in a higher (32% vs 9%) likelihood of remission at 8 weeks."
Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis (2016): http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0157259
Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis (2017). Pooled rate of clinical remission in all 4 trials was 42.1% in the group receiving donor FMT and 22.6% in those receiving control: https://sci-hub.tw/http://journals.lww.com/ibdjournal/Abstract/2017/10000/Systematic_Review_and_Meta_analysis___Fecal.5.aspx
The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis (2017): http://onlinelibrary.wiley.com/doi/10.1111/apt.14387/abstract
Fecal microbiome from patients with ulcerative colitis is potent to induce inflammatory responses. "fecal bacteria from UC patients cause stronger inflammatory responses than fecal bacteria from healthy controls" (2018): https://www.sciencedirect.com/science/article/pii/S1567576918301589
"FMT from UC donors to normal recipient rats triggered UC symptoms, UC-prone microbial shift, and host metabolic adaption" (2018): http://aem.asm.org/content/early/2018/04/30/AEM.00434-18.abstract
Microbiome profiling reveals associations with ulcerative colitis severity, treatment. Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course (Oct 2018): https://medicalxpress.com/news/2018-10-microbiome-profiling-reveals-associations-ulcerative.html - https://doi.org/10.1016/j.chom.2018.09.009
IBS:
Numerous studies & reviews:
https://old.reddit.com/r/ibs/search?q=author%3Amaximiliankohler&restrict_sr=on&sort=relevance&t=all
https://old.reddit.com/r/ibs/comments/8hwqed/a_list_of_studies_i_believe_to_be_important_for/ - https://archive.li/xlft2
A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies (2018). Summary of dysbiosis findings in IBS (Table 1): https://link.springer.com/article/10.1007%2Fs12325-018-0673-5#Sec3 - "There is growing evidence indicating that fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) may result in bloating, pain and other IBS symptoms in approximately 70% of IBS patients"
The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation (Nov 2018). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194904 "Patients’ microbiota profiles became more-or-less similar to donors. Questionnaire scores were significantly improved at all time points following FMT"
Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial (2018): https://archive.fo/YDfsm
Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis (2017): http://dx.doi.org/10.1016/j.dld.2017.01.142 - http://www.sciencedirect.com/science/article/pii/S1590865817301469
Review, 2017: We highlight the known effects of gut microbiota on mechanisms implicated in the pathophysiology of IBS including disrupted gut brain axis (GBA), visceral hypersensitivity (VH), altered GI motility, epithelial barrier dysfunction and immune activation /r/ibs/comments/5ezg3f
Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome (2017): http://www.gastrojournal.org/article/S0016-5085(16)35174-5/fulltext
Fecal transplants from humans with irritable bowel syndrome and anxiety into mice lead to similar symptoms and anxiety-like behavior in the rodents, researchers report (2017): https://archive.fo/cbQBn
Fecal microbiota transplantation in patients with slow-transit constipation: A randomized, clinical trial. (2017): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291446/
Up to 50% of cases of chronic diahrrea/IBS-D is Bile Acid Malabsorption: https://archive.is/pfH3P - and bile acid absorption & metabolism is mediated by gut microbes: /s/HumanMicrobiome/wiki/bile
Norwegian medical researchers have shown that the intestines of IBS patients do react to food in a special way (2014): http://sciencenordic.com/first-image-irritable-bowel
Removing fiber from diet decreases constipation symptoms and increases BM frequency (2012): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435786/
Immune system:
https://old.reddit.com/s/HumanMicrobiome/wiki/immunesystem
Inflammation & arthritis:
Gut bacteria can cause, predict and prevent rheumatoid arthritis: http://www.eurekalert.org/pub_releases/2016-07/mc-sgb071116.php
Review, 2017: Role of Gut Microbiota in Rheumatoid Arthritis. "In summary, Prevotella species are involved in the pathogenesis of arthritis." http://www.mdpi.com/2077-0383/6/6/60/htm
Review, 2017: Role of Gut Microbiota in Rheumatoid Arthritis: http://www.mdpi.com/2077-0383/6/6/60
Review, 2016: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions: http://www.nature.com/nrrheum/journal/vaop/ncurrent/full/nrrheum.2016.68.html
Review, 2016: How the microbiota shapes rheumatic diseases: http://www.nature.com/nrrheum/journal/vaop/ncurrent/full/nrrheum.2016.85.html
Review, 2016: Microbiota and Arthritis: Correlations or Cause? https://www.ncbi.nlm.nih.gov/pubmed/26814405 - http://www.medscape.com/viewarticle/858691_1 - http://www.medscape.com/viewarticle/858691_3
The Microbiome in Pediatric Rheumatic Diseases: http://www.the-rheumatologist.org/article/microbiome-pediatric-rheumatic-diseases/
Two rheumatoid arthritis–specific autoantigens correlate microbial immunity with autoimmune responses in joints. In rheumatoid arthritis (RA), immunological triggers at mucosal sites, such as the gut microbiota, may promote autoimmunity that affects joints. (plus many more in comments): /r/HumanMicrobiome/comments/6jxd4i
Oregon study suggests some gut microbes may be keystones of health. "The inflammatory response in the third fish was completely controlled by the low-abundance species": https://around.uoregon.edu/content/oregon-study-suggests-some-gut-microbes-may-be-keystones-health
How gut bacteria affects the brain and body: http://big.assets.huffingtonpost.com/2015_GutBacteriaA.png
Role of the Gut Microbiome in Modulating Arthritis Progression in Mice: http://www.nature.com/articles/srep30594
Bones and the Biome: The Link Between Our Microbiota and Rheumatologic Disease: http://www.medscape.com/viewarticle/859725
Impact of the gut microbiota on inflammation, obesity, and metabolic disease: http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0303-2 - http://www.nature.com/cti/journal/v5/n4/full/cti201612a.html
If being too clean makes us sick, why isn’t getting dirty the solution? https://theconversation.com/if-being-too-clean-makes-us-sick-why-isnt-getting-dirty-the-solution-50572 (says getting dirty generally makes inflammation worse)
Gout:
Intestinal Microbiota Distinguish Gout Patients from Healthy Humans: http://www.nature.com/articles/srep20602
Kidney:
Review, 2019: Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights: https://doi.org/10.1093/advances/nmy068
Review, 2019: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease: https://doi.org/10.1186/s12967-018-1756-4
Review, 2018: The gut microbiota and the brain–gut–kidney axis in hypertension and chronic kidney disease https://www.nature.com/articles/s41581-018-0018-2
Review, 2018: Mitochondrial dysfunction and gut microbiota imbalance: An intriguing relationship in chronic kidney disease https://doi.org/10.1016/j.mito.2018.11.006
Review, 2018: Altered microbiome in chronic kidney disease: systemic effects of gut-derived uremic toxins http://www.clinsci.org/content/132/5/509
Review, 2018: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients https://doi.org/10.1111/nep.13452
Review, 2016: Gut hormones and gut microbiota: implications for kidney function and hypertension https://doi.org/10.1016/j.jash.2016.10.007
Kidneys sniff out signals from gut bacteria for cues to moderate blood pressure after meals https://www.quantamagazine.org/how-bacteria-help-regulate-blood-pressure-20171130/
Liver:
Review, 2018: Liver–Microbiome Axis in Health and Disease. "a liver–microbiome bidirectional crosstalk appears to be critical in health and various liver diseases and could be therapeutically targeted, such as by fecal microbiota transplantation" /r/HumanMicrobiome/comments/8mxwyb
Review, 2018: The gut–liver axis and the intersection with the microbiome https://www.nature.com/articles/s41575-018-0011-z
Review, 2017: The gut microbiome and liver cancer: mechanisms and clinical translation: /r/HumanMicrobiome/comments/6m0rms
Single bacterial strain causes liver damage: Enterobacter cloacae B29 administration induces hepatic damage and subcutaneous fat accumulation in high-fat diet fed mice (2018): http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0198262
Microbial metabolite contributes to the accumulation of lipids in the liver and hence to nonalcoholic steatohepatitis (2018): https://www.nature.com/articles/s41591-018-0126-3
Gut microbiota translocation promotes autoimmune cholangitis (2018): https://doi.org/10.1016/j.jaut.2018.09.010 "our data demonstrates the important role of gut microbiota and bacterial translocation in the pathogenesis of murine autoimmune cholangitis"
How gut bacteria may help to spot and address liver disease (2018): https://www.medicalnewstoday.com/articles/322269.php
Study finds gut microbiome can control antitumor immune function in liver. "if you treat mice with antibiotics and thereby deplete certain bacteria, you can change the composition of immune cells of the liver [due to bile acid changes], affecting tumor growth in the liver" (2018): /r/HumanMicrobiome/comments/8m4fh4
Gut microbiome composition in lean patients with NASH (nonalcoholic fatty liver disease) is associated with liver damage independent from caloric intake: a prospective pilot study (2018): https://www.sciencedirect.com/science/article/pii/S0939475317302417
Fecal Transplant Efficacy Examined for Chronic Liver Disease. Fecal microbiota transplantation (FMT) from a rationally selected donor seems safe and effective for patients with primary sclerosing cholangitis (PSC) (2017): /r/HumanMicrobiome/comments/76tgzr
Probiotics Prevent Autoimmune-Related Liver Injury. A recent study examined the effect of Lactobacillus probiotic strains on liver injury in lupus-prone mice, demonstrating that gut bacteria plays an important role in autoimmune diseases. (2017) /r/HumanMicrobiome/comments/6oa3in
Genetically Obese Human Gut Microbiota Induces Liver Steatosis in Germ-Free Mice Fed on Normal Diet (2018): https://www.frontiersin.org/articles/10.3389/fmicb.2018.01602/full
Fecal microbiota transplant improves brain function in hepatic encephalopathy (2018): https://www.healio.com/hepatology/cirrhosis-liver-failure/news/online/%7bf51c9fa5-2a7d-4a01-8810-2fa94ba245be%7d/fecal-microbiota-transplant-improves-brain-function-in-hepatic-encephalopathy
Microbiota Control of Malaria, Dengue, and Zika:
Bacteria Block Mosquitoes from Transmitting Zika, Brazilian Study Says. Wolbachia bacteria have already been used to control dengue: http://www.scientificamerican.com/article/bacteria-block-mosquitoes-from-transmitting-zika-brazilian-study-says/
Wolbachia Bacteria Could Be Answer To Malaria, Dengue: Bill Gates: http://www.ndtv.com/health/wolbachia-bacteria-could-be-answer-to-malaria-dengue-bill-gates-1280579
Microbiota Control of Malaria Transmission: http://dx.doi.org/10.1016/j.pt.2015.11.004
Composition of the gut microbiota modulates the severity of malaria: http://www.pnas.org/content/113/8/2235
More effects of antibiotics:
Review, 2018: Antibiotics and autoimmune and allergy diseases: Causative factor or treatment? https://www.sciencedirect.com/science/article/pii/S1567576918304752 "Antibiotics use in children promotes the development of allergic disorders, whereas antibiotics use in adults seems to ameliorate inflammatory responses and reduce the severity of autoimmune diseases"
Review, 2018: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome http://www.ijmedrev.com/article_76662.html "Short-term antibiotic treatment is able to change the richness and diversity of species into a long-term dysbiotic state"
Review, 2018: Antibiotics and the nervous system: More than just the microbes? https://doi.org/10.1016/j.bbi.2018.12.014 "clinical as well as experimental literature, largely neglected through the past decade, has clearly demonstrated that broad classes of antibiotics are neuroactive or neurotoxic. This is true even for some antibiotics that are widely regarded as not absorbed in the intestinal tract"
Review, 2017: Antibiotic use and microbiome function: http://www.sciencedirect.com/science/article/pii/S0006295216302866
Some of the changes caused by antibiotics are transient and can be reversed at the end of the treatment, while others seem irreversible. Most importantly, it has been observed that gut bacteria present a lower capacity to produce proteins, as well as display deficiencies in key activities, during and after the antibiotic treatment. For instance, antibiotics decrease the ability to absorb iron, to digest certain foods and to produce essential molecules. Previously it was assumed that short-term antibiotic treatment would alter gut microbe composition only for a short time, however, this is not the case. Even a relatively short course of antibiotics can lead to alteration in gut microbiota, which in turn can lead to severe consequences such as inflammation, immune dysregulation, allergies, infections, cardiovascular diseases, diabetes, metabolic issues, GI disease such as Crohn’s, IBD, yeast overgrowth, chronic constipation and diarrhea (2018) https://www.frontiersin.org/articles/10.3389/fncel.2018.00256/full#h4
Antibiotic Scars Left on the Gut Microbiota from the Stringent Response (2018): https://www.cell.com/trends/microbiology/fulltext/S0966-842X(18)30138-0 - "Current research is primarily focused on compositional shifts and alterations in the metabolic status of the gut microbiota to elucidate the damage caused by antibiotics. However, the impact of the stringent response, which is governed by a global gene regulatory system conserved in most gut bacteria, should not be overlooked."
"Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome" (2018): https://msphere.asm.org/content/3/6/e00588-18
Pre-transplant recovery of microbiome diversity without recovery of the original microbiome (2018): https://sci-hub.tw/https://www.nature.com/articles/s41409-018-0414-z "our findings suggest that recovery of diversity alone is not an adequate surrogate for microbiome recovery. Microbiota composition and its potential functionality should be considered along with diversity in drawing conclusions from microbiome studies"
Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans (Nov 2018) https://academic.oup.com/jac/advance-article-abstract/doi/10.1093/jac/dky471/5173727 "combined treatment with broad-spectrum antibiotics has a profound & long-lasting effect on microbiota composition, the consequences of which remain largely unknown"
"expansion of a certain species of house dust fungus (Wallemia mellicola) can occur in the intestines of mice after they are treated with antibiotics and exposed to the fungus. By contrast, mice with an intact and healthy intestinal microbiota resist this expansion. After expansion of this fungal population, the mice are more prone to develop asthma-like inflammation in their lungs when exposed to allergens" https://www.eurekalert.org/pub_releases/2018-09/p-gfe091318.php
"We identified valerate as a metabolite that is depleted with clindamycin and only recovered with FMT." https://www.gastrojournal.org/article/S0016-5085(18)34771-1/fulltext "Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota (2018)"
Substantial reduction in microbiota diversity in subjects who took either amoxicillin or azithromycin and that those reductions were sustained throughout the 6-month study (2016): http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0187-9
Early life antibiotic exposure affects pancreatic islet development and metabolic regulation. Changes in the expression of key genes involved in short-chain fatty acid signaling and pancreatic development were detected in later life (2017): http://www.nature.com/articles/srep41778
Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior (2017): https://www.nature.com/articles/ncomms15062
Infant antibiotic use linked to adult diseases (2015): https://www.sciencedaily.com/releases/2015/05/150513140929.htm - Antibiotics, Pediatric Dysbiosis, and Disease http://dx.doi.org/10.1016/j.chom.2015.04.006
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic (ciprofloxacin) perturbation (2011): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3063582/
Antibiotics that kill gut bacteria also stop growth of new brain cells: https://www.sciencedaily.com/releases/2016/05/160519130105.htm
Antibiotics impair murine hematopoiesis by depleting intestinal microbiota (2016): https://doi.org/10.1182/blood-2016-03-708594
Bactericidal Antibiotics Induce Mitochondrial Dysfunction and Oxidative Damage in Mammalian Cells (2013): http://dx.doi.org/10.1126/scitranslmed.3006055
Inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. Kill intestinal epithelium cells (2015): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5166700/ - https://www.medicalnewstoday.com/articles/289259.php
Linked to Sepsis risk (2016): http://www.medpagetoday.com/meetingcoverage/idweek/61073
Encourage spread of c.diff to people who haven't taken antibiotics (2016): https://medicalresearch.com/author-interviews/antibiotics-encourage-spread-c-diff-patients-havent-received-antibiotics/28609
Reduces gut diversity of housemates who haven’t taken antibiotics: http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0187-9 Microbial diversity in individuals and their household contacts following typical antibiotic courses (2016).
Negative impact on the phageome; low doses can make phages go extinct by making bacteria resistant to them (2016): https://archive.is/lHdQG
In antibiotics-treated mice, serotonin, tryptophan hydroxylase 1, and secondary bile acids levels were decreased: https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-016-1105-4 Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility (2017).
Antibiotics found to weaken body's ability to fight off disease: https://www.eurekalert.org/pub_releases/2017-08/uovh-aft081717.php
A single early-life macrolide antibiotic course can alter the microbiota and modulate host immune phenotypes that persist long after exposure has ceased (2017): https://www.nature.com/articles/s41467-017-00531-6
Association between prior antibiotic therapy and subsequent risk of community-acquired infections: a systematic review (2017): https://academic.oup.com/jac/advance-article-abstract/doi/10.1093/jac/dkx374/4629206
This mouse study suggests FMT may not completely restore immune function damaged by antibiotics (2017): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395657/ "Immune Responses to Broad-Spectrum Antibiotic Treatment and Fecal Microbiota Transplantation in Mice"
Depletion of the gut microbiome by antibiotics impairs the body's ability to eliminate toxins like arsenic and mercury.
More studies showing long-term negative affects here: /s/HumanMicrobiome/wiki/maternity and by using the "antibiotics" flair in the sidebar.
Skin:
revision by MaximilianKohlerreads microbiomedigest.com daily— view source
