Rapid evolution and strain turnover in the infant gut microbiome

Genome Research, Journal Year: 2022, Volume and Issue: 32(6), P. 1124 - 1136

Published: May 11, 2022

Although the ecological dynamics of infant gut microbiome have been intensely studied, relatively little is known about evolutionary in microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over first year life find that microbiomes are distinct those adults. We evidence for a 10-fold increase rate evolution strain turnover compared with healthy adults, mother-infant transition at delivery being particularly dynamic period which gene loss dominates. Within few months after birth, these stabilize, gains become increasingly frequent as matures. furthermore changes show signatures seeded by mixture de novo mutations transmissions pre-evolved lineages broader family. Several occur parallel across infants, highlighting candidate genes may play important roles development Our results point to picture volatile characterized rapid change early days life.

Language: Английский

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Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(28)

Published: July 5, 2022

The genetic composition of the gut microbiota is constantly reshaped by ecological and evolutionary forces. These strain-level dynamics are challenging to understand because they depend on complex spatial growth processes that take place within a host. Here we introduce population framework predict how stochastic forces emerge from simple models microbial in spatially extended environments like intestinal lumen. Our shows fluid flow longitudinal variation rate combine shape frequencies variants simulated fecal samples, yielding analytical expressions for effective generation times, selection coefficients, rates drift. We find over longer timescales, emergent can often be captured well-mixed lack explicit structure, even when there substantial species-level composition. By applying these results human colon, continuous forms wall alone unlikely create sufficient bottlenecks allow large fluctuations mutant also times may significantly shorter than expected traditional average estimates. provide starting point quantifying turnover settings relevant other ecosystems where unidirectional plays an important role.

Language: Английский

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Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 119(1)

Published: Dec. 28, 2021

Significance The human body harbors numerous and diverse bacteria, the vast majority of which are located in gut. These bacteria can mutate evolve within gut, is their natural environment. This have important public health implications (e.g., when gut antibiotic resistance). features specific characteristics, including hydrodynamic flow resulting gradients food bacterial concentrations. How do these characteristics impact evolution diversity bacteria? We demonstrate that they substantially increase probability neutral mutants reach high proportions eventually take over population. because only a fraction actively dividing. Thus, environment enhances diversity.

Language: Английский

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Microbial experimental evolution in a massively multiplexed and high-throughput era

Current Opinion in Genetics & Development, Journal Year: 2022, Volume and Issue: 75, P. 101943 - 101943

Published: June 22, 2022

Experimental evolution with microbial model systems has transformed our understanding of the basic rules underlying ecology and evolution. Experiments leveraging as a central feature put evolutionary theories to test, modern sequencing engineering tools then characterized molecular basis adaptation. As theory experimentations refined evolution, need increase throughput experimental complexity emerged. Here, we summarize recent technologies that have made high-throughput experiments practical highlight studies capitalized on these tools, defining an exciting new era in Multiple research directions previously limited by scale are now accessible for study believe applying lessons from vitro onto applied settings potential major innovations discoveries across medicine.

Language: Английский

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A macroecological perspective on genetic diversity in the human gut microbiome

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(7), P. e0288926 - e0288926

Published: July 21, 2023

While the human gut microbiome has been intensely studied, we have yet to obtain a sufficient understanding of genetic diversity that it harbors. Research efforts demonstrated considerable fraction within-host variation in is driven by ecological dynamics co-occurring strains belonging same species, suggesting an lens may provide insight into empirical patterns diversity. Indeed, model self-limiting growth and environmental noise known as Stochastic Logistic Model (SLM) was recently shown successfully predict temporal within single host. However, its ability across hosts be tested. In this manuscript I determine whether predictions SLM explain unrelated for 22 common microbial species. Specifically, stationary distribution explains allele frequencies predicts harboring given (i.e., prevalence) sites. The accuracy correlated with independent estimates strain structure, follow statistically similar forms due existence strain-level ecology.

Language: Английский

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Rapid evolution and strain turnover in the infant gut microbiome

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Sept. 27, 2021

ABSTRACT While the ecological dynamics of infant gut microbiome have been intensely studied, relatively little is known about evolutionary in microbiome. Here we analyze longitudinal fecal metagenomic data from >700 infants and their mothers over first year life find that microbiomes are distinct adults. We evidence for almost 100-fold increase rate evolution strain turnover compared to healthy adults, with mother-infant transition at delivery being a particularly dynamic period which gene loss dominates. Within few months after birth, these stabilize, gains become increasingly frequent as matures. furthermore changes show signatures seeded by mixture de novo mutations transmissions pre-evolved lineages broader family. Several occur parallel multiple infants, highlighting candidate genes may play important roles development Our results point picture volatile characterized rapid change early days life.

Language: Английский

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Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: May 16, 2021

Abstract The gut microbiota features important genetic diversity, and the specific spatial of may shape evolution within this environment. We investigate fixation probability neutral bacterial mutants a minimal model that includes hydrodynamic flow resulting gradients food concentrations. find is substantially increased compared to an equivalent well-mixed system, in regime where profiles concentration are strongly spatially-dependent. Fixation then becomes independent total population size. show our results can be rationalized by introducing active population, which consists those bacteria actively consuming dividing. size yields effective for mutant gut. Significance statement human body harbors numerous diverse bacteria, vast majority located These mutate evolve gut, their natural This have public health implications, e.g. when antibiotic resistance. characteristics, including How do these characteristics impact diversity bacteria? demonstrate they increase reach high proportions eventually take over population. because only fraction Thus, environment enhances diversity.

Language: Английский

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