Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.

The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.

Gut-microbiota-targeted diets modulate human immune status.

Diet modulates the gut microbiome, which in turn can impact the immune system. Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, we found diet-specific effects. The high-fiber diet increased microbiome-encoded glycan-degrading carbohydrate active enzymes (CAZymes) despite stable microbial community diversity. Although cytokine response score (primary outcome) was unchanged, three distinct immunological trajectories in high-fiber consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society.

Impacts of a novel defensive symbiosis on the nematode host microbiome.

BACKGROUND: Bacteria adapted to live within animals can protect their hosts against harmful infections. Beyond antagonism with pathogens, a 'defensive' bacterial symbiont could engage in additional interactions with other colonizing micro-organisms. A single bacterium might thus have cascading ecological impacts on the whole microbiome that are rarely investigated. Here, we assess the role of a defensive symbiont as a driver of host-associated microbiota composition by using a bacterial species (Enterococcus faecalis) that was previously experimentally adapted to a nematode host model (Caenorhabditis elegans). RESULTS: An analysis of 16S rRNA data from C. elegans exposed to E. faecalis and subsequently reared in soil, reveal that symbiont adaptation to host environment or its protective potential had minimal impact on microbiota diversity. Whilst the abundance of Pseudomonas was higher in the microbiota of hosts with protective E.faecalis (and another protective species tested), a few other genera - including Serratia and Salinispora - were less abundant in hosts colonized by all E. faecalis strains. In addition, the protective effect of E. faecalis against virulent Staphylococcus aureus pathogens was maintained despite multi-species interactions within the microbiota. CONCLUSIONS: Our results reveal the degree to which a new, evolving symbiont can colonise and maintain pathogen-resistance with minimal disruption to host microbiota diversity.

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.

Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes.

The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.

Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.

Invasive freshwater snails form novel microbial relationships.

Resident microbes (microbiota) can shape host organismal function and adaptation in the face of environmental change. Invasion of new habitats exposes hosts to novel selection pressures, but little is known about the impact on microbiota and the host-microbiome relationship (e.g., how rapidly new microbial associations are formed, whether microbes influence invasion success). We used high-throughput 16S rRNA sequencing of New Zealand (native) and European (invasive) populations of the freshwater snail Potamopyrgus antipodarum and found that while invaders do carry over some core microbial taxa from New Zealand, their microbial community is largely distinct. This finding highlights that invasions can result in the formation of novel host-microbiome relationships. We further show that the native microbiome is composed of fewer core microbes than the microbiome of invasive snails, suggesting that the microbiota is streamlined to a narrower set of core members. Furthermore, native snails exhibit relatively low alpha diversity but high inter-individual variation, whereas invasive snails have higher alpha diversity but are relatively similar to each other. Together, our findings demonstrate that microbiota comparisons across native and invasive populations can reveal the impact of a long coevolutionary history and specialization of microbes in the native host range, as well as new associations occurring after invasion. We lay essential groundwork for understanding how microbial relationships affect invasion success and how microbes may be utilized in the control of invasive hosts.

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish.

Exposure to environmental toxins such as heavy metals can perturb the development and stability of microbial communities associated with human or animal hosts. Widespread arsenic contamination in rivers and riparian habitats therefore presents environmental and health concerns for populations living near sources of contamination. To investigate how arsenic affects host microbiomes, we sequenced and characterized the microbiomes of twenty larval zebrafish exposed to three concentrations of arsenic that are found in contaminated water-low (10 ppb), medium (50 ppb), and high (100 ppb) for 20 days. We found that even a small concentration of arsenic changed the overall microbial composition, structure and diversity of microbial communities, causing dysbiosis in developing larval zebrafish microbiota. In addition, we found that a high concentration of arsenic also increased the abundance of a class 1 integron, an integrase-dependent system facilitating the horizontal transfer of genes conferring resistance to heavy metals and antibiotics.

Mutual fitness benefits arise during coevolution in a nematode-defensive microbe model.

Species interactions can shift along the parasitism-mutualism continuum. However, the consequences of these transitions for coevolutionary interactions remain unclear. We experimentally coevolved a novel species interaction between Caenorhabditis elegans hosts and a mildly parasitic bacterium, Enterococcus faecalis, with host-protective properties against virulent Staphylococcus aureus. Coinfections drove the evolutionary transition of the C. elegans-E. faecalis relationship toward a reciprocally beneficial interaction. As E. faecalis evolved to protect nematodes against S. aureus infection, hosts adapted by accommodating greater numbers of protective bacteria. The mutualism was strongest in pairings of contemporary coevolved populations. To generally assess the conditions under which these defensive mutualisms can arise and coevolve, we analyzed a model that showed that they are favored when mild parasites confer an intermediate level of protection. Our results reveal that coevolution can shape the transition of animal-parasite interactions toward defensive symbioses in response to coinfections.

Dysbiosis and early mortality in zebrafish larvae exposed to subclinical concentrations of streptomycin.

Exposure to low concentrations of antibiotics found in aquatic environments can increase susceptibility to infection in adult fish due to microbiome disruption. However, little is known regarding the effect of antibiotic pollution on fish larvae. Here, we show that exposure to streptomycin, a common antibiotic used in medicine and aquaculture, disrupts the normal composition of zebrafish larvae microbiomes, significantly reducing the microbial diversity found in the fish. Exposure to streptomycin also significantly increased early mortality among fish larvae, causing full mortality within a few days of exposure at 10 µg/mL. Finally, we found that subclinical concentrations of streptomycin also increased the abundance of class 1 integrons, an integrase-dependent genetic system associated to the horizontal transfer of antibiotic resistance genes, in the larvae microbiomes. These results suggest that even low concentrations of streptomycin associated with environmental pollution could impact fish populations and lead to the creation of antibiotic resistance reservoirs.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.

BACKGROUND: The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants. RESULTS: Over 2832 swabs, wipes, and air samples were collected from 16 private-style NICU rooms housing very low birth weight (< 1500 g), premature (< 31 weeks' gestation) infants. For each infant, room samples were collected daily, Monday through Friday, for 1 month. The first samples from the first infant and the last samples from the last infant were collected 383 days apart. Twenty-two NICU locations spanning room surfaces, hands, electronics, sink basins, and air were collected. Results point to an incredibly simple room community where 5-10 taxa, mostly skin-associated, account for over 50% of the amplicon reads. Biomass estimates reveal four to five orders of magnitude difference between the least to the most dense microbial communities, air, and sink basins, respectively. Biomass trends from bioaerosol samples and petri dish dust collectors suggest occupancy to be a main driver of suspended biological particles within the NICU. Using a machine learning algorithm to classify the origin of room samples, we show that each room has a unique microbial fingerprint. Several important taxa driving this model were dominant gut colonizers of infants housed within each room. CONCLUSIONS: Despite regular cleaning of hospital surfaces, bacterial biomass was detectable at varying densities. A room-specific microbiome signature was detected, suggesting microbes seeding NICU surfaces are sourced from reservoirs within the room and that these reservoirs contain actively dividing cells. Collectively, the data suggests that hospitalized infants, in combination with their caregivers, shape the microbiome of NICU rooms.