Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: May 21, 2021

Abstract Background In gut microbiome studies, the cultured microbial resource plays essential roles, such as helping to unravel functions and host-microbe interactions. Although several major studies have been performed elucidate human microbiota, up 70% of Unified Human Gastrointestinal Genome species not date. Large-scale isolation identification well availability public are imperative for further characterizing functions. Results this study, we constructed a Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn ) through cultivation 10,558 isolates from 31 sample mixtures 239 fresh fecal samples healthy Chinese volunteers, deposited 1170 strains representing 400 different in culture collections International Depository Authority long-term preservation access worldwide. Following rules Code Nomenclature Prokaryotes, 102 new were characterized denominated, while 28 genera 3 families proposed. hGMB represented over 80% common dominant global 16S rRNA gene amplicon data ( n = 11,647) 24 “most-wanted” “medium priority” taxa proposed by Microbiome Project. We total sequenced 115 genomes novel 13 previously known species. Further silico analysis revealed that newly 22 uncultured (UHGG) contributed representatives potentially “dark taxa” had discovered UHGG. The nonredundant catalogs generated covered 50% functionally genes (KEGG orthologs) largest approximately 10% “most wanted” unknown proteins FUnkFams database. Conclusions A publicly accessible (hGMB) was established contained represents expands resources genomic repository adding species, genera, families, microbes.

Language: Английский

---

How Probiotics Affect the Microbiota

Frontiers in Cellular and Infection Microbiology, Journal Year: 2020, Volume and Issue: 9

Published: Jan. 15, 2020

Probiotics have been used to treat a variety of diseases for decades: however, what is the rationale under this? Such treatment was first proposed in early 19th century based on observations decreased Bifidobacteria populations children suffering diarrhea, suggesting that oral intake could replete microbiota subpopulation and improve health. Since then, studies shown modifications gut or skin course suggested positive effects certain probiotics. Most failed report any impact microbiota. The probiotics, as well bacteria colonizing food, does not reside their ability graft but rather sharing genes metabolites, supporting challenged microbiota, by direct influence epithelial immune cells. argue probiotics be associated conventional drugs insulin resistance, infectious diseases, inflammatory psychiatric disorders also interfere with drug metabolism. Nevertheless, context plethora probiotic strains associations, produced such conditions do allow comparisons, it remains difficult know whether patient would benefit from taking particular probiotic. In other words, although several mechanisms are observed when studying single strain, all individual expected share same effects. order clarify role clinics, we explore here relation between

Language: Английский

---

Nutritional psychiatry: Towards improving mental health by what you eat

European Neuropsychopharmacology, Journal Year: 2019, Volume and Issue: 29(12), P. 1321 - 1332

Published: Nov. 14, 2019

Does it matter what we eat for our mental health? Accumulating data suggests that this may indeed be the case and diet nutrition are not only critical human physiology body composition, but also have significant effects on mood wellbeing. While determining factors of health complex, increasing evidence indicates a strong association between poor exacerbation disorders, including anxiety depression, as well other neuropsychiatric conditions. There common beliefs about certain foods supported by solid scientific demonstrating unequivocal link is beginning to emerge. Current epidemiological do provide information causality or underlying mechanisms. Future studies should focus elucidating mechanism. Randomized controlled trials high quality, adequately powered geared towards advancement knowledge from population-based observations personalized nutrition. Here, an overview emerging field nutritional psychiatry, exploring exemplifying importance well-balanced health. We conclude experimental medicine approach mechanistic understanding required which future policies can based.

Language: Английский

---

Depression's Unholy Trinity: Dysregulated Stress, Immunity, and the Microbiome

Annual Review of Psychology, Journal Year: 2019, Volume and Issue: 71(1), P. 49 - 78

Published: Sept. 30, 2019

Depression remains one of the most prevalent psychiatric disorders, with many patients not responding adequately to available treatments. Chronic or early-life stress is key risk factors for depression. In addition, a growing body data implicates chronic inflammation as major player in depression pathogenesis. More recently, gut microbiota has emerged an important regulator brain and behavior also been linked However, how this holy trinity interact maintain physiological homeostasis fully understood. review, we integrate from animal human studies on these three etiology progression We focus processes by which microbiota-immune-stress matrix may influence centrally mediated events possible therapeutic interventions correct imbalances triune.

Language: Английский

---

Vulnerability of the industrialized microbiota

Science, Journal Year: 2019, Volume and Issue: 366(6464)

Published: Oct. 24, 2019

One world, one health As people increasingly move to cities, their lifestyles profoundly change. Sonnenburg and review how the shift of recent generations from rural, outdoor environments urbanized industrialized settings has affected our biology health. The signals change are seen most strikingly in reduction commensal microbial taxa loss metabolic functions. extirpation human commensals is a result bombardment by new chemicals, foodstuffs, sanitation, medical practices. For people, sanitation readily available food have been beneficial, but we now reached tipping point? How do “conserve” beneficial symbionts keep pathogens at bay? Science , this issue p. eaaw9255

Language: Английский

---

Nurturing Nature: How Brain Development Is Inherently Social and Emotional, and What This Means for Education

Educational Psychologist, Journal Year: 2019, Volume and Issue: 54(3), P. 185 - 204

Published: July 3, 2019

New advances in neurobiology are revealing that brain development and the learning it enables directly dependent on social-emotional experience. Growing bodies of research reveal importance socially triggered epigenetic contributions to network configuration, with implications for functioning, cognition, motivation, learning. Brain is also impacted by health-related physical developmental factors, such as sleep, toxin exposure, puberty, which turn influence functioning cognition. An appreciation dynamic interdependencies experience, underscores a "whole child" approach education reform leads important insights To facilitate these interdisciplinary conversations, here we conceptualize within framework current evidence fundamental ubiquitous biological constraints affordances undergirding learning–related constructs more broadly. Learning indeed depends how nature nurtured.

Language: Английский

---

Microbial transmission in animal social networks and the social microbiome

Nature Ecology & Evolution, Journal Year: 2020, Volume and Issue: 4(8), P. 1020 - 1035

Published: June 22, 2020

Language: Английский

---

The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt's hypothesis revisited

˜The œLancet. Gastroenterology & hepatology, Journal Year: 2019, Volume and Issue: 4(12), P. 984 - 996

Published: Nov. 4, 2019

Language: Английский

---

Association of the Gut Microbiota With Cognitive Function in Midlife

JAMA Network Open, Journal Year: 2022, Volume and Issue: 5(2), P. e2143941 - e2143941

Published: Feb. 8, 2022

Animal experiments and small clinical studies support a role for the gut microbiota in cognitive functioning. Few have investigated cognition large community samples.To examine associations of microbial composition with measures an established population-based study middle-aged adults.This cross-sectional analyzed data from prospective Coronary Artery Risk Development Young Adults (CARDIA) cohort 4 US metropolitan centers between 2015 2016. Data were 2019 2020.Stool DNA sequenced, following gathered: (1) β-diversity (between-person) derived multivariate principal coordinates analysis; (2) α-diversity (within-person), defined as richness (genera count) Shannon index (integrative measure genera evenness); (3) taxonomy (107 genera, after filtering).Cognitive status was assessed using 6 clinic-administered tests: Montreal Cognitive Assessment (MoCA), Digit Symbol Substitution Test (DSST), Rey-Auditory Verbal Learning (RAVLT), Stroop, category fluency, letter fluency. A global score components analysis also assessed; first component explained 56% variability.Microbiome available on 597 CARDIA participants; mean (SD) age 55.2 (3.5) years, 268 participants (44.7%) men, 270 (45.2%) Black. In multivariable-adjusted analysis, permutational variance tests statistically significant all (principal P = .001; MoCA, DSST, RAVLT, .007; .001) exception fluency (P .07). After adjusting sociodemographic variables (age, race, sex, education), health behaviors (physical activity, diet, smoking, medication use), covariates (body mass index, diabetes, hypertension), Barnesiella positively associated (β, 0.16; 95% CI, 0.08-0.24), DSST 1.18; 0.35-2.00), 0.59; 0.31-0.87); Lachnospiraceae FCS020 group 2.67; 1.10-4.23), Sutterella negatively MoCA -0.27; -0.44 to -0.11).In this study, composition, based β-diversity, analysis. These contribute growing body literature suggesting that may be aging, but must replicated larger samples further researched identify relevant pathways.

Language: Английский

---

Microbial transmission in the social microbiome and host health and disease

Cell, Journal Year: 2024, Volume and Issue: 187(1), P. 17 - 43

Published: Jan. 1, 2024

Language: Английский

---