The Long-Term Stability of the Human Gut Microbiota

Abstract

A low-error 16S rRNA amplicon sequencing method (LEA-Seq) plus whole genome sequencing of >500 cultured isolates were used to characterize bacterial strain composition in the fecal microbiota of 37 USA adults sampled for up to five years. Microbiota stability follows a power law function which, when extrapolated, suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members, but not from unrelated individuals. Sampling individuals for up to 32 weeks while consuming a monotonous liquid diet indicated that changes in weight are more predictive of changes in strain composition than sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

“…All omic levels exhibited individuality and family specificity, which has previously been described only for metagenomes [3][4][5] . The observed individual patterns in relation to secreted human proteins may well be an important factor shaping the gastrointestinal microbiome, culminating in the observed individuality.…”

“…In addition to community stability, the persistence of individualspecific strains has been documented 4,5 . To explore whether strain specificity also translates to the functional level, we analysed the encoded functional potential and corresponding expression profiles of closely related reconstructed genomes recovered from different samples.…”

“…etagenomic studies of faecal samples have provided deep insights into the structure and functional potential of microbial communities within the human gastrointestinal tract 1,2 , revealing their inter-individual variability 3 and apparent intra-individual stability 4,5 . Case-control studies have associated microbial traits in individuals with patterns of diseases, thereby implicating gastrointestinal microbial communities in a range of human disorders [6][7][8][9][10] .…”

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

“…In other systems ranging from hydra to fish and mice, closely related hosts harbor more similar microbial communities than do more distantly related individuals (Zoetendal et al, 2001;Friswell et al, 2010;Navarrete et al, 2012;Faith et al, 2013;Franzenburg et al, 2013). The ongoing discovery of particular loci that shape the gut microbiome in model organisms (Benson et al, 2010) presents an intriguing target for future studies across animal systems in both the lab and field.…”

Organisms or biological individuals? Combining physiological and evolutionary individuality

“…But it is important to recognise that a major result of recent biological research is precisely that very often a physiological individual is not as such a reproducing entity, but rather a local nexus of different lineages of reproducing entities. Indeed, work on symbiosis has shown that virtually all physiological individuals are multispecies units (Pradeu and Carosella 2006;Dupré and O'Malley 2009;Bosch and McFall-Ngai 2011;Pradeu 2012), functionallyintegrated wholes that unify an extraordinarily diverse range of living constituents -in particular bacteria (Bäckhed et al 2005;Faith et al 2013), fungi (Underhill andIliev 2014), andviruses (Virgin 2014). Such a physiological whole does not include as its constituents all the microbes that are in or on the host, only those that both interact strongly with other host's constituents and make a critical contribution to the functioning and survival of the whole.…”