The comings and goings of the healthy human gut microbiota

SNP-level analysis of 5,000+ metagenomic samples enabled Hildebrand et al., 2021Hildebrand F. Gossmann T.I. Frioux C. Özkurt E. Myers P.N. Ferretti P. Kuhn M. Bahram Nielsen H.B. Bork Dispersal strategies shape persistence and evolution human gut bacteria.Cell Host Microbe. 2021; 29 (S1931-3128(21)00236-5)https://doi.org/10.1016/j.chom.2021.05.008Abstract Full Text PDF Scopus (14) Google Scholar to identify microbiota by their dispersal in this issue Cell & This brings us a step closer understanding how microbial communities are formed maintained also hints at ways which microbiomes can be manipulated improve health. A remarkable aspect the microbiome healthy individual is just stable it is. Despite daily changes food sources, alcohol consumption, sleeping habits, other behaviors shown affect composition, barring major perturbations (e.g., antibiotics or infection), 90% strains persist over year roughly 60% 5 years (Faith 2013Faith J.J. Guruge J.L. Charbonneau Subramanian S. Seedorf H. Goodman A.L. Clemente J.C. Knight R. Heath A.C. Leibel R.L. al.The long-term stability microbiota.Science. 2013; 341: 1237439Crossref PubMed (1139) Scholar). Stability itself thought an important characteristic feature gut, promoting both resistance infection resilience. finding now quite robust with more extensive sequencing efforts recent advances bioinformatics assembly SNP-calling developments. observation prompts follow-up question—how maintained? Numerous host-derived factors contribute stability, including host behaviors, genetics, immune pressures. Yet, species may harbor specific traits that confer via dispersal, colonization, maintenance (Figure 1). Whereas often assessed as gross metric describing community time, colleagues, Microbe, turned attention toward classifying steadfast versus volatile (Hildebrand By analyzing than 5,000 metagenomes, they were able organisms high (durable colonization), resilience (repeated lower across individuals. In addition accounting for these functional attributes, assembled genomes has allowed polymorphism-level examination evolutionary evidence within (i.e., rates non-synonymous synonymous mutation, effective population size, bottlenecks) further disentangle strains. signatures, well geographic familial distribution strains, next label bacterial archeael whether exploit vertical horizontal modes transmission. clades bacteria identified colleagues consistent those found several previous studies. The archeae Methanobrevibacter, find heredipersistence, been previously circulate among twin siblings (Goodrich 2014Goodrich J.K. Waters Poole Sutter Koren O. Blekhman Beaumont Van Treuren W. Bell J.T. al.Human genetics microbiome.Cell. 2014; 159: 789-799Abstract (1638) Scholar); Bacteroides species, “tenacious,” term use describe persistent phylogeography transmission, tend transmitted vertically even wild mice (Moeller 2018Moeller A.H. Suzuki T.A. Phifer-Rixey Nachman M.W. Transmission mammalian 2018; 362: 453-457Crossref (105) extend observations 400 well-represented highlighted—oxygen tolerance sporulation—are promote environment additional hosts therefore greater dependence on transmission paths. wider variety likely involved aspects persistence. Some favor single route, such genes pH osmotic stress responses attachment type particle; colonization require certain adhesion factors; involve evasion, metabolism, antagonism, suggest few. Seminal studies addressing question have applied powerful knock-in knock-out approaches. For example, screening approach mucin polysaccharide utilization, response pathways, promoted murine (Crook 2019Crook N. Ferreiro A. Gasparrini A.J. Pesesky Gibson M.K. Wang B. Sun X. Condiotte Z. Dobrowolski Peterson D. Dantas G. Adaptive Strategies Candidate Probiotic coli Nissle Mammalian Gut.Cell 2019; 25: 499-512.e8Abstract (40) suggests causes tenacity known enrichment carbohydrate utilization loci. Transposon mutagenesis microbes introduced into mouse harboring simplified revealed nutrient competition most (Goodman 2009Goodman McNulty N.P. Zhao Y. Leip Mitra R.D. Lozupone C.A. Gordon J.I. Identifying genetic determinants needed establish symbiont its habitat.Cell 2009; 6: 279-289Abstract (436) Such experiments bridging what we know about bestow pathogens enhanced features exploited commensals gut. Equipped characterization bacteria, ask specifics regarding microbiota. inter-personal microbes? Daily sampling shows punctuated events illness result large numbers replacement events, but dietary shifts do not (David 2014David L.A. Materna Friedman J. Campos-Baptista M.I. Blackburn M.C. Perrotta Erdman S.E. Alm E.J. lifestyle affects timescales.Genome Biol. 15: R89Crossref (485) And groups? Evidence from fecal transplantation closely related colonize together (Smillie 2018Smillie C.S. Sauk Gevers Sung Youngster I. Hohmann E.L. Staley Khoruts Sadowsky M.J. al.Strain Tracking Reveals Determinants Bacterial Engraftment Human Gut Following Fecal Microbiota Transplantation.Cell 23: 229-240.e5Abstract (149) Re-analysis findings light newly defined categories prompt investigation mechanisms fostering knowing follow heredipersistent spatiopersistent help explain predict observed first- second-generation immigrants (Vangay 2018Vangay Johnson Ward T.L. Al-Ghalith G.A. Shields-Cutler R.R. Hillmann B.M. Lucas S.K. Beura L.K. Thompson E.A. Till L.M. al.US Immigration Westernizes Microbiome.Cell. 175: 962-972.e10Abstract (272) Likewise, will determine role play patients various diseases. authors show children acquire increasing number until around age 10, furthering notion long-held serve “second genome.” But long-standing homeostasis, framework compositional context disease? aging (Wilmanski 2021Wilmanski T. Diener Rappaport Patwardhan Wiedrick Lapidus Earls Zimmer Glusman Robinson al.Gut pattern reflects ageing predicts survival humans.Nat Metab. 3: 274-286Crossref (64) Scholar), inflamed differ widely rely orthogonal set maintained. obtaining better grasp host-microbiota interactions, leveraged health interventions. Tenacious define levels family geography, higher patterns adaptation. At same susceptible antibiotic perturbations. These include abundant members microbiome, genera Prevotella. postulate easier replace post-antibiotic exposure, suggesting selected genetically modified successfully implemented Lactobacilli, exhibit Overall, microbiota, terms taxa ultimately play, inform our knowledge aid designing therapeutic manipulations communities. bacteriaHildebrand al.Cell MicrobeJune 9, 2021In BriefHildebrand investigated using publicly available time series metagenomes stool samples. They three underlie distinct accumulation rare variation differences strength selection. Full-Text Open Access