Systematic Review of Gut Microbiota and Major Depression

Stephanie G. Cheung1,2, Ariel Goldenthal1,3, Anne‐Catrin Uhlemann4,5, J. John Mann1,6,3, Jeffrey M. Miller1,3, M. Elizabeth Sublette1,3
1Department of Psychiatry, Columbia University, New York, NY, United States
2Division of Consultation-Liaison Psychiatry, Columbia University, New York, NY, United States
3Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
4Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, United States
5Microbiome & Pathogen Genomics Core, Columbia University, New York, NY, United States
6Department of Radiology, Columbia University, New York, NY, United States

Tóm tắt

Từ khóa


Tài liệu tham khảo

Gotlib, 2009, Handbook of Depression

2017, Depression and Other Common Mental Disorders: Global Health Estimates, 1

2017, Depression Fact Sheet.

Dean, 2017, The neurobiology of depression: an integrated view, Asian J Psychiatry, 27, 101, 10.1016/j.ajp.2017.01.025

Lederberg, 2001, “Ome sweet” omics: a genealogical treasury of words, TheScientist, 15, 8

Tannock, 2017, Understanding the Gut Microbiota., 10.1002/9781118801413

Hara, 2006, The gut flora as a forgotten organ, EMBO Rep., 7, 688, 10.1038/sj.embor.7400731

Ait-Belgnaoui, 2012, Prevention of gut leakiness by a probiotic treatment leads to attenuated HPA response to an acute psychological stress in rats, Psychoneuroendocrinology, 37, 1885, 10.1016/j.psyneuen.2012.03.024

Barrett, 2012, γ-Aminobutyric acid production by culturable bacteria from the human intestine, J Appl Microbiol., 113, 411, 10.1111/j.1365-2672.2012.05344.x

Cummings, 1987, Short chain fatty acids in human large intestine, portal, hepatic and venous blood, Gut, 28, 1221, 10.1136/gut.28.10.1221

Hooper, 2003, Angiogenins: a new class of microbicidal proteins involved in innate immunity, Nat Immunol., 4, 269, 10.1038/ni888

Schauber, 2003, Expression of the cathelicidin LL-37 is modulated by short chain fatty acids in colonocytes: relevance of signalling pathways, Gut, 52, 735, 10.1136/gut.52.5.735

Cash, 2006, Symbiotic bacteria direct expression of an intestinal bactericidal lectin, Science, 313, 1126, 10.1126/science.1127119

Bouskra, 2008, Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis, Nature, 456, 507, 10.1038/nature07450

Smith, 2013, The microbial metabolites, short chain fatty acids, regulate colonic Treg cell homeostasis, Science, 341, 569, 10.1126/science.1241165.

Miyamoto, 2015, A gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, ameliorates intestinal epithelial barrier impairment partially via GPR40-MEK-ERK pathway, J Biol Chem., 290, 2902, 10.1074/jbc.M114.610733

Maes, 2008, The gut-brain barrier in major depression: intestinal mucosal dysfunction with an increased translocation of LPS from gram negative enterobacteria, (leaky gut) plays a role in the inflammatory pathophysiology of depression, Neuro Endocrinol Lett., 29, 117

Maes, 2012, Increased IgA and IgM responses against gut commensals in chronic depression: further evidence for increased bacterial translocation or leaky gut, J Affect Disord., 141, 55, 10.1016/j.jad.2012.02.023

Maes, 2013, In depression, bacterial translocation may drive inflammatory responses, oxidative and nitrosative stress, (O&NS), and autoimmune responses directed against O&NS-damaged neoepitopes, Acta Psychiatr Scand., 127, 344, 10.1111/j.1600-0447.2012.01908.x

Guida, 2018, Antibiotic-induced microbiota perturbation causes gut endocannabinoidome changes, hippocampal neuroglial reorganization and depression in mice, Brain Behav Immun., 67, 230, 10.1016/j.bbi.2017.09.001

Clarke, 2013, The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner, Mol Psychiatry, 18, 666, 10.1038/mp.2012.77

Kelly, 2016, Transferring the blues: depression-associated gut microbiota induces neurobehavioural changes in the rat, J Psychiatr Res., 82, 109, 10.1016/j.jpsychires.2016.07.019

Zheng, 2016, Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism, Mol Psychiatry, 21, 786, 10.1038/mp.2016.44

Mi, 2015, Effectiveness of Lactobacillus reuteri in infantile colic and colicky induced maternal depression: a prospective single blind randomized trial, Antonie van Leeuwenhoek, 107, 1547, 10.1007/s10482-015-0448-9

Hsiao, 2013, Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders, Cell, 155, 1451, 10.1016/j.cell.2013.11.024

Naseribafrouei, 2014, Correlation between the human fecal microbiota and depression, Neurogastroenterol Motil, 26, 1155, 10.1111/nmo.12378

Jiang, 2015, Altered fecal microbiota composition in patients with major depressive disorder, Brain Behav Immun., 48, 186, 10.1016/j.bbi.2015.03.016

Aizawa, 2016, Possible association of Bifidobacterium and Lactobacillus in the gut microbiota of patients with major depressive disorder, J Affect Disord., 202, 254, 10.1016/j.jad.2016.05.038

Lin, 2017, Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder, J Affect Disord., 207, 300, 10.1016/j.jad.2016.09.051

Chen, 2018, Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder, Neuroreport, 29, 417, 10.1097/WNR.0000000000000985

Hawinkel, 2017, A broken promise: microbiome differential abundance methods do not control the false discovery rate, Brief Bioinform, 20, 210, 10.1093/bib/bbx104

Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science, 334, 105, 10.1126/science.1208344

McDonald, 2018, American Gut: an open platform for citizen science microbiome research, mSystems, 3, e00031, 10.1128/mSystems.00031-18

He, 2018, Regional variation limits applications of healthy gut microbiome reference ranges and disease models, Nat Med., 24, 1532, 10.1038/s41591-018-0164-x

Davey, 2013, Antipsychotics and the gut microbiome: olanzapine-induced metabolic dysfunction is attenuated by antibiotic administration in the rat, Transl Psychiatry, 3, e309, 10.1038/tp.2013.83

Morgan, 2014, The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse, PLoS ONE, 9, e115225, 10.1371/journal.pone.0115225

Bahr, 2015, Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure, EBioMedicine, 2, 1725, 10.1016/j.ebiom.2015.10.018

Flowers, 2017, Interaction between atypical antipsychotics and the gut microbiome in a bipolar disease cohort, Pharmacotherapy, 37, 261, 10.1002/phar.1890

Thomas, 2010, Probiotics-host communication: modulation of signaling pathways in the intestine, Gut Microbes, 1, 148, 10.4161/gmic.1.3.11712

Hemarajata, 2013, Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation, Therap Adv Gastroenterol., 6, 39, 10.1177/1756283X12459294

Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821

Spencer, 2011, Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency, Gastroenterology, 140, 976, 10.1053/j.gastro.2010.11.049

Huttenhower, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234

Yadav, 2018, A review of metabolic potential of human gut microbiome in human nutrition, Arch Microbiol., 200, 203, 10.1007/s00203-017-1459-x

Kamada, 2013, Control of pathogens and pathobionts by the gut microbiota, Nat Immunol., 14, 685, 10.1038/ni.2608

Lyte, 2013, Microbial endocrinology in the microbiome-gut-brain axis: how bacterial production and utilization of neurochemicals influence behavior, PLoS Pathogens, 9, e1003726, 10.1371/journal.ppat.1003726

Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540

Haghikia, 2015, Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine, Immunity, 43, 817, 10.1016/j.immuni.2015.09.007

Koh, 2016, From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites, Cell, 165, 1332, 10.1016/j.cell.2016.05.041

Zimmerman, 2012, Butyrate suppresses colonic inflammation through HDAC1-dependent Fas upregulation and Fas-mediated apoptosis of T cells, Am J Physiol., 302, G1405, 10.1152/ajpgi.00543.2011

Kamada, 2013, Role of the gut microbiota in immunity and inflammatory disease, Nat Rev Immunol., 13, 321, 10.1038/nri3430

Singh, 2014, Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis, Immunity, 40, 128, 10.1016/j.immuni.2013.12.007

Fuchikami, 2016, The potential use of histone deacetylase inhibitors in the treatment of depression, Prog Neuropsychopharmacol Biol Psychiatry, 64, 320, 10.1016/j.pnpbp.2015.03.010

DeCastro, 2005, Short chain fatty acids regulate tyrosine hydroxylase gene expression through a cAMP-dependent signaling pathway, Mol Brain Res., 142, 28, 10.1016/j.molbrainres.2005.09.002

Wu, 2008, Histone deacetylase inhibitors up-regulate astrocyte GDNF and BDNF gene transcription and protect dopaminergic neurons, Int J Neuropsychopharmacol., 11, 1123, 10.1017/S1461145708009024

Kidd, 2010, Protection of dopaminergic cells from MPP+-mediated toxicity by histone deacetylase inhibition, Brain Res., 1354, 172, 10.1016/j.brainres.2010.07.041

Wall, 2014, Bacterial neuroactive compounds produced by psychobiotics, Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease., 221, 10.1007/978-1-4939-0897-4_10

Sheydina, 2014, Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase, BMC Bioinformatics, 15, 112, 10.1186/1471-2105-15-112

Duranti, 2015, Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum, Environ Microbiol., 17, 2515, 10.1111/1462-2920.12743

Liu, 2015, Starch and starch hydrolysates are favorable carbon sources for bifidobacteria in the human gut, BMC Microbiol., 15, 54, 10.1186/s12866-015-0362-3

Khoroshkin, 2016, Transcriptional regulation of carbohydrate utilization pathways in the bifidobacterium genus, Front Microbiol., 7, 120, 10.3389/fmicb.2016.00120

Ozcan, 2017, A human gut commensal ferments cranberry carbohydrates to produce formate, Appl Environ Microbiol, 10.1128/AEM.01097-17

Chung, 2017, Prebiotic potential of pectin and pectic oligosaccharides to promote anti-inflammatory commensal bacteria in the human colon, FEMS Microbiol Ecol., 10.1093/femsec/fix127

Tan, 2010, Novel alpha-glucosidase from human gut microbiome: substrate specificities and their switch, FASEB J, 24, 3939, 10.1096/fj.10-156257

Mao, 2015, In vitro fermentation of fructooligosaccharides with human gut bacteria, Food Funct., 6, 947, 10.1039/C4FO01082E

Morais, 2016, Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition, Environ Microbiol., 18, 542, 10.1111/1462-2920.13047

Hehemann, 2012, Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes, Proc Natl Acad Sci USA., 109, 19786, 10.1073/pnas.1211002109

Zhang, 2014, Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes, Proc Natl Acad Sci USA., 111, E3708, 10.1073/pnas.1406156111

Pudlo, 2015, Symbiotic human gut bacteria with variable metabolic priorities for host mucosal glycans, MBio, 6, e01282, 10.1128/mBio.01282-15

Despres, 2016, Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis, BMC Genomics, 17, 147, 10.1186/s12864-016-2472-1

Rakoff-Nahoum, 2016, The evolution of cooperation within the gut microbiota, Nature, 533, 255, 10.1038/nature17626

Tauzin, 2016, Molecular dissection of xyloglucan recognition in a prominent human gut symbiont, MBio, 7, e02134, 10.1128/mBio.02134-15

Tauzin, 2016, Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli, Mol Microbiol., 102, 579, 10.1111/mmi.13480

Ali-Ahmad, 2017, Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2, J Struct Biol., 197, 227, 10.1016/j.jsb.2016.11.004

Costliow, 2017, Thiamine acquisition strategies impact metabolism and competition in the gut microbe bacteroides thetaiotaomicron, mSystems, 2, e00116, 10.1128/mSystems.00116-17

Ndeh, 2017, Complex pectin metabolism by gut bacteria reveals novel catalytic functions, Nature, 544, 65, 10.1038/nature21725

Temple, 2017, A Bacteroidetes locus dedicated to fungal 1,6-beta-glucan degradation: unique substrate conformation drives specificity of the key endo-1,6-beta-glucanase, J Biol Chem., 292, 10639, 10.1074/jbc.M117.787606

Praharaj, 2018, Molecular dynamics insights into the structure, function, and substrate binding mechanism of mucin desulfating sulfatase of gut microbe Bacteroides fragilis, J Cell Biochem., 119, 3618, 10.1002/jcb.26569

Sato, 2017, Prebiotic potential of L-sorbose and xylitol in promoting the growth and metabolic activity of specific butyrate-producing bacteria in human fecal culture, FEMS Microbiol Ecol., 93, fiw227, 10.1093/femsec/fiw227

Plichta, 2016, Transcriptional interactions suggest niche segregation among microorganisms in the human gut, Nat Microbiol., 1, 16152, 10.1038/nmicrobiol.2016.152

Van den Abbeele, 2013, Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model, ISME J, 7, 949, 10.1038/ismej.2012.158

Grondin, 2017, Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens, PLoS ONE, 12, e0171606, 10.1371/journal.pone.0171606

Caminero, 2014, Diversity of the cultivable human gut microbiome involved in gluten metabolism: isolation of microorganisms with potential interest for coeliac disease, FEMS Microbiol Ecol., 88, 309, 10.1111/1574-6941.12295

Kaur, 2017, In silico analysis of putrefaction pathways in bacteria and its implication in colorectal cancer, Front Microbiol., 8, 2166, 10.3389/fmicb.2017.02166

McLuskey, 2016, Crystal structure and activity studies of the C11 cysteine peptidase from parabacteroides merdae in the human gut microbiome, J Biol Chem., 291, 9482, 10.1074/jbc.M115.706143

Sanctuary, 2018, Dietary considerations in autism spectrum disorders: the potential role of protein digestion and microbial putrefaction in the gut-brain axis, Front Nutr., 5, 40, 10.3389/fnut.2018.00040

Wolfe, 2011, Dietary protein and protein-rich food in relation to severely depressed mood: A 10 year follow-up of a national cohort, Prog Neuropsychopharmacol Biol Psychiatry, 35, 232, 10.1016/j.pnpbp.2010.11.011

Pooyan, 2018, A high-protein/low-fat diet may interact with vitamin D-binding protein gene variants to moderate the risk of depression in apparently healthy adults, Lifestyle Genom., 11, 64, 10.1159/000492497

Bhandari, 2017, Association of Inflammatory Bowel Disease, (IBD) with depressive symptoms in the United States population and independent predictors of depressive symptoms in an IBD population: a NHANES study, Gut Liver, 11, 512, 10.5009/gnl16347

Said, 2011, Intestinal absorption of water-soluble vitamins in health and disease, Biochem J., 437, 357, 10.1042/BJ20110326

Kwak, 2016, Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function, Syst Appl Microbiol., 39, 429, 10.1016/j.syapm.2016.07.004

Gilbody, 2007, Is low folate a risk factor for depression? A meta-analysis and exploration of heterogeneity, J Epidemiol Community Health, 61, 631, 10.1136/jech.2006.050385

Beydoun, 2010, Serum folate, vitamin B-12, and homocysteine and their association with depressive symptoms among U.S. adults, Psychosom Med., 72, 862, 10.1097/PSY.0b013e3181f61863

Kumar, 1997, A protein-tyrosine kinase-regulated, pH-dependent, carrier-mediated uptake system for folate in human normal colonic epithelial cell line NCM460, J Biol Chem., 272, 6226, 10.1074/jbc.272.10.6226

Dudeja, 1997, Evidence for the existence of a carrier-mediated folate uptake mechanism in human colonic luminal membranes, Am J Physiol., 272, G1408

Zhang, 2013, Thiamine nutritional status and depressive symptoms are inversely associated among older Chinese adults, J Nutr., 143, 53, 10.3945/jn.112.167007

Said, 2004, Recent advances in carrier-mediated intestinal absorption of water-soluble vitamins, Annu Rev Physiol., 66, 419, 10.1146/annurev.physiol.66.032102.144611

Paerl, 2018, Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis, Sci Rep., 8, 5940, 10.1038/s41598-018-24321-2

Pinto-Sanchez, 2015, Anxiety and depression increase in a stepwise manner in parallel with multiple FGIDs and symptom severity and frequency, Am J Gastroenterol., 110, 1038, 10.1038/ajg.2015.128

Rao, 2011, Comparison of small bowel and colonic mucosal permeability in ulcerative/microscopic colitis, irritable bowel syndrome-diarrhea, and healthy controls by urinary saccharide excretion measurements, Gastroenterology, 140, S707, 10.1016/S0016-5085(11)62938-7

Vivinus-Nebot, 2012, Combination of allergic factors can worsen diarrheic irritable bowel syndrome: role of barrier defects and mast cells, Am J Gastroenterol., 107, 75, 10.1038/ajg.2011.315

Kassinen, 2007, The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects, Gastroenterology, 133, 24, 10.1053/j.gastro.2007.04.005

Ye, 2006, Molecular mechanism of tumor necrosis factor-α modulation of intestinal epithelial tight junction barrier, Am J Physiol., 290, G496, 10.1152/ajpgi.00318.2005

Bischoff, 2014, Intestinal permeability–a new target for disease prevention and therapy, BMC Gastroenterol., 14, 189, 10.1186/s12876-014-0189-7

Wei, 1986, O2 radicals in arachidonate-induced increased blood-brain barrier permeability to proteins, Am J Physiol., 251, H693

Easton, 1998, Arachidonic acid increases cerebral microvascular permeability by free radicals in single pial microvessels of the anaesthetized rat, J Physiol., 507, 541, 10.1111/j.1469-7793.1998.541bt.x

Marchiando, 2011, The epithelial barrier is maintained by in vivo tight junction expansion during pathologic intestinal epithelial shedding, Gastroenterology, 140, 1208, 10.1053/j.gastro.2011.01.004

Maes, 1998, The effects of psychological stress on humans: increased production of pro-inflammatory cytokines and a Th1-like response in stress-induced anxiety, Cytokine, 10, 313, 10.1006/cyto.1997.0290

Miura, 2008, A link between stress and depression: shifts in the balance between the kynurenine and serotonin pathways of tryptophan metabolism and the etiology and pathophysiology of depression, Stress, 11, 198, 10.1080/10253890701754068

Schwarcz, 1983, Quinolinic acid: an endogenous metabolite that produces axon-sparing lesions in rat brain, Science, 219, 316, 10.1126/science.6849138

Guillemin, 2012, Quinolinic acid, the inescapable neurotoxin, FEBS J, 279, 1356, 10.1111/j.1742-4658.2012.08485.x

Williams, 2014, Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine, Cell Host Microbe, 16, 495, 10.1016/j.chom.2014.09.001

Yunes, 2016, GABA production and structure of gadB/gadC genes in Lactobacillus and Bifidobacterium strains from human microbiota, Anaerobe, 42, 197, 10.1016/j.anaerobe.2016.10.011

O'Mahony, 2015, Serotonin, tryptophan metabolism and the brain-gut-microbiome axis, Behav Brain Res., 277, 32, 10.1016/j.bbr.2014.07.027

Liu, 2016, Alteration of behavior and monoamine levels attributable to Lactobacillus plantarum PS128 in germ-free mice, Behav Brain Res., 298, 202, 10.1016/j.bbr.2015.10.046

Bercik, 2011, The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut–brain communication, Neurogastroenterol Motil., 23, 1132, 10.1111/j.1365-2982.2011.01796.x

Bravo, 2011, Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve, Proc Natl Acad Sci USA., 108, 16050, 10.1073/pnas.1102999108

Fernandez-Real, 2015, Gut Microbiota Interacts With Brain Microstructure and Function, J Clin Endocrinol Metab., 100, 4505, 10.1210/jc.2015-3076

Tillisch, 2017, Brain structure and response to emotional stimuli as related to gut microbial profiles in healthy women, Psychosom Med., 79, 905, 10.1097/PSY.0000000000000493

Tillisch, 2013, Consumption of fermented milk product with probiotic modulates brain activity, Gastroenterology, 144, 1394, 10.1053/j.gastro.2013.02.043

Pinto-Sanchez, 2017, Probiotic Bifidobacterium longum NCC3001 reduces depression scores and alters brain activity: a pilot study in patients with irritable bowel syndrome, Gastroenterology, 153, 448, 10.1053/j.gastro.2017.05.003

Yoshioka, 1983, Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants, Pediatrics, 72, 317, 10.1542/peds.72.3.317

Lin, 2010, A meta-analytic review of polyunsaturated fatty acid compositions in patients with depression, Biol Psychiatry, 68, 140, 10.1016/j.biopsych.2010.03.018

Liu, 2015, Pathways of polyunsaturated fatty acid utilization: implications for brain function in neuropsychiatric health and disease, Brain Res., 1597, 220, 10.1016/j.brainres.2014.11.059

Kankaanpää, 2001, The influence of polyunsaturated fatty acids on probiotic growth and adhesion, FEMS Microbiol Lett., 194, 149, 10.1111/j.1574-6968.2001.tb09460.x

Bomba, 2002, Improvement of the probiotic effect of micro-organisms by their combination with maltodextrins, fructo-oligosaccharides and polyunsaturated fatty acids, Br J Nutr., 88, S95, 10.1079/BJN2002634

Ohtsuka, 1997, Reducing cell membrane n-6 fatty acids attenuate mucosal damage in food-sensitive enteropathy in mice, Pediatr Res., 42, 835, 10.1203/00006450-199712000-00019

Druart, 2014, Gut microbial metabolites of polyunsaturated fatty acids correlate with specific fecal bacteria and serum markers of metabolic syndrome in obese women, Lipids, 49, 397, 10.1007/s11745-014-3881-z

Raimondi, 2016, Conjugated linoleic acid production by bifidobacteria: screening, kinetic, and composition, Biomed Res Int., 2016, 8654317, 10.1155/2016/8654317

Kim, 2017, Current state and applications of microbial genome-scale metabolic models, Curr Opin Syst Biol., 2, 10, 10.1016/j.coisb.2017.03.001

Bordbar, 2014, Constraint-based models predict metabolic and associated cellular functions, Nat Rev Genet., 15, 107, 10.1038/nrg3643

McCloskey, 2013, Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli, Mol Syst Biol., 9, 661, 10.1038/msb.2013.18

Quince, 2017, Shotgun metagenomics, from sampling to analysis, Nat Biotechnol., 35, 833, 10.1038/nbt.3935

Korem, 2015, Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples, Science, 349, 1101, 10.1126/science.aac4812

Maier, 2018, Extensive impact of non-antibiotic drugs on human gut bacteria, Nature, 555, 623, 10.1038/nature25979

Cueva, 2017, An integrated view of the effects of wine polyphenols and their relevant metabolites on gut and host health, Molecules, 22, E99, 10.3390/molecules22010099

Falony, 2016, Population-level analysis of gut microbiome variation, Science, 352, 560, 10.1126/science.aad3503

Zhernakova, 2016, Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity, Science, 352, 565, 10.1126/science.aad3369

Turner, 2015, Loss of δ-catenin function in severe autism, Nature, 520, 51, 10.1038/nature14186

Pullabhatla, 2018, De novo mutations implicate novel genes in systemic lupus erythematosus, Hum Mol Genet., 27, 421, 10.1093/hmg/ddx407

Shankar, 2017, Insights into study design and statistical analyses in translational microbiome studies, Ann Transl Med., 5, 249, 10.21037/atm.2017.01.13

Hamilton, 1960, A rating scale for depression, J Neurol Neurosurg Psychol., 23, 56, 10.1136/jnnp.23.1.56

Beck, 1961, An inventory for measuring depression, Arch Gen Psychiatry, 4, 53, 10.1001/archpsyc.1961.01710120031004

Guenther, 2013, Update of the healthy eating index: HEI-2010, J Acad Nutr Diet, 113, 569, 10.1016/j.jand.2012.12.016

Bowyer, 2018, Use of dietary indices to control for diet in human gut microbiota studies, Microbiome, 6, 77, 10.1186/s40168-018-0455-y

Cenit, 2017, Influence of gut microbiota on neuropsychiatric disorders, World J Gastroenterol., 23, 5486, 10.3748/wjg.v23.i30.5486

Vuong, 2017, Emerging roles for the gut microbiome in autism spectrum disorder, Biol Psychiatry, 81, 411, 10.1016/j.biopsych.2016.08.024

Nguyen, 2018, Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder, J Psychiatr Res., 99, 50, 10.1016/j.jpsychires.2018.01.013

Swidsinski, 2005, Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice, World J Gastroenterol., 11, 1131, 10.3748/wjg.v11.i8.1131

Nani, 2017, Changes in salivary microbiota increase volatile sulfur compounds production in healthy male subjects with academic-related chronic stress, PLoS ONE, 12, e0173686, 10.1371/journal.pone.0173686

Lamb, 2017, Elevated salivary IgA, decreased anxiety, and an altered oral microbiota are associated with active participation on an undergraduate athletic team, Physiol Behav., 169, 169, 10.1016/j.physbeh.2016.12.004

Qiao, 2018, Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls, Sci Rep., 8, 1597, 10.1038/s41598-018-19982-y

Gonzalez, 2016, Migraines are correlated with higher levels of Nitrate-, Nitrite-, and Nitric Oxide-reducing oral microbes in the american gut project cohort, mSystems, 1, 1, 10.1128/mSystems.00105-16