Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling

AbstractThe gut microbiome starts to be shaped in the first days of life and continues to increase its diversity during the first months. Several investigations are assessing the link between the configuration of the infant gut microbiome and infant health, but a comprehensive strain-level assessment of vertically transmitted microbes from mother to infant is still missing. We longitudinally collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life, and applied shotgun metagenomic sequencing followed by strain-level profiling. We observed several specific strains including those from Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, that were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo expression of vertically transmitted microbes, for example Bacteroides vulgatus and Bifidobacterium spp., thus suggesting that transmitted strains are functionally active in the two rather different environments of the adult and infant guts. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we showed that it is possible to track vertical transmission of members of the microbiome from mother to infants and characterize their transcriptional activity. Our work poses the basis for surveying at larger scale the sources of microbial diversity in the infants and starts associating these transmissions with the subsequent longer-term development of a healthy or dysbiotic microbiome.ImportanceEarly infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support that the maternal microbial reservoir is a key route of microbial transmission, yet much is inferred from the observation of shared species in mother and infant. Common species, per se, does not necessarily equate vertical transmission as species exhibit considerable strain heterogeneity and it is therefore imperative to identify shared strains. We demonstrate here the potential of shotgun metagenomics and strain-level resolution to identify vertical transmission events via the maternal source. Combined with a metatranscriptomic approach, we show the potential not only to identify and track the fate of microbes in the early infant microbiome but also identify the metabolically active members. These approaches will ultimately provide important insights into the acquisition, development and community dynamics of the infant microbiome.

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Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

mSystems ◽

10.1128/msystems.00164-16 ◽

2017 ◽

Vol 2 (1) ◽

Cited By ~ 130

Author(s):

Francesco Asnicar ◽

Serena Manara ◽

Moreno Zolfo ◽

Duy Tin Truong ◽

Matthias Scholz ◽

...

Keyword(s):

Vertical Transmission ◽

Community Dynamics ◽

Common Species ◽

Strain Level ◽

Shotgun Metagenomics ◽

Content Type ◽

Infant Exposure ◽

Early Infant ◽

As Species ◽

Considerable Strain

ABSTRACT Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome. The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.

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Impacts of the Marine Hatchery Built Environment on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola Lalandi

10.21203/rs.3.rs-75521/v1 ◽

2020 ◽

Author(s):

Jeremiah Minich ◽

Barbara Nowak ◽

Abigail Elizur ◽

Rob Knight ◽

Stewart Fielder ◽

...

Keyword(s):

Built Environment ◽

Vertical Transmission ◽

Marine Fish ◽

Gut Microbiome ◽

Community Dynamics ◽

Animal Health ◽

Rrna Gene ◽

Yellowtail Kingfish ◽

Seriola Lalandi ◽

Microbiome Development

Abstract BackgroundMicrobial succession in vertebrates has primarily focused on vertical transmission and ontogenetic development in the mammalian gut. Teleosts comprise the majority of vertebrate diversity, yet little is known about how the microbiome develops in fish, particularly when vertical transmission is limited or absent for broadcast spawners. Biological factors such as diet, age, phylogeny, and trophic level along with environmental factors such as water salinity, temperature, and depth have been shown to influence the mucosal microbiomes of fish. Here we investigate how various microbial-rich surfaces from the built environment ‘BE’ influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time.ResultsFor the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish microbiomes (gill, skin, and digesta) and the BE (tank side, water, inlet pipe, airstones, and air diffusers) were sampled from indoor reared fish at three ages (43 dph, 137 dph, 430 dph; n=12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. We quantified the change in community dynamics driven by the BE and show that the gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut microbiome becomes increasingly differentiated from the environment over time.ConclusionsOur findings suggest that fish mucosal microbiomes are differentially influenced by the built environment with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to stressors in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.

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Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic and functional diversity

10.1101/2021.04.30.442084 ◽

2021 ◽

Author(s):

Rachel Gilroy ◽

Joy Leng ◽

Anuradha Ravi ◽

Evelien M Adriaenssens ◽

Aharon Oren ◽

...

Keyword(s):

Functional Diversity ◽

Gut Microbiome ◽

Metagenomic Sequencing ◽

Shotgun Metagenomics ◽

High Fiber ◽

Functional Studies ◽

Fiber Diet ◽

Faecal Samples ◽

Culture Independent ◽

Medium Quality

Background: The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fiber diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. Results: We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic and functional diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes. Conclusions: Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.

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Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome

mSphere ◽

10.1128/msphere.00694-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Louis-Marie Bobay ◽

Emily F. Wissel ◽

Kasie Raymann

Keyword(s):

Microbial Communities ◽

Honey Bee ◽

Deep Sequencing ◽

Gut Microbiome ◽

Cost Effective ◽

Whole Genome Shotgun ◽

Strain Level ◽

Whole Genome ◽

Metagenomic Sequencing ◽

Microbiome Composition

ABSTRACT Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes. IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.

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Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly

BMC Bioinformatics ◽

10.1186/s12859-019-3073-1 ◽

2019 ◽

Vol 20 (S16) ◽

Author(s):

Joyce B. Kang ◽

Benjamin A. Siranosian ◽

Eli L. Moss ◽

Niaz Banaei ◽

Tessa M. Andermann ◽

...

Keyword(s):

Resistance Genes ◽

Gut Microbiome ◽

Draft Genome ◽

Strain Level ◽

Comparative Genomic ◽

Metagenomic Sequencing ◽

Antibiotic Exposure ◽

E Coli ◽

Selective Pressures ◽

Antimicrobial Resistance Genes

Abstract Background Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure. Results Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject’s gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject’s E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli. Conclusion This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.

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Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch

BMC Veterinary Research ◽

10.1186/s12917-021-02815-y ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Yuting Liu ◽

Bo Liu ◽

Chengwu Liu ◽

Yumiao Hu ◽

Chang Liu ◽

...

Keyword(s):

Bacterial Diversity ◽

Gut Microbiome ◽

Bacterial Flora ◽

Antibiotic Resistance Genes ◽

Living Environment ◽

Domestic Dogs ◽

Metagenomic Sequencing ◽

Shotgun Metagenomics ◽

Clinical Drugs ◽

And Function

Abstract Background Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared with captive wolves. We surveyed the gut bacterial diversity of 27 domestic dogs, which were fed commercial dog food, and 31 wolves, which were fed uncooked meat, by 16S rRNA sequencing. In addition, we collected fecal samples from 5 dogs and 5 wolves for shotgun metagenomic sequencing to explore changes in the functions of their gut microbiome. Results Differences in the abundance of core bacterial genera were observed between dogs and wolves. Together with shotgun metagenomics, the gut microbiome of dogs was found to be enriched in bacteria resistant to clinical drugs (P < 0.001), while wolves were enriched in bacteria resistant to antibiotics used in livestock (P < 0.001). In addition, a higher abundance of putative α-amylase genes (P < 0.05; P < 0.01) was observed in the dog samples. Conclusions Living environment of dogs and domestic wolves has led to increased numbers of bacteria with antibiotic resistance genes, with exposure to antibiotics through direct and indirect methods. In addition, the living environment of dogs has allowed the adaptation of their microbiota to a starch-rich diet. These observations align with a domestic lifestyle for domestic dogs and captive wolves, which might have consequences for public health.

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Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults

Genes ◽

10.3390/genes12030331 ◽

2021 ◽

Vol 12 (3) ◽

pp. 331

Author(s):

Nachon Raethong ◽

Massalin Nakphaichit ◽

Narissara Suratannon ◽

Witida Sathitkowitchai ◽

Wanlapa Weerapakorn ◽

...

Keyword(s):

Gut Microbiome ◽

Asian Country ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Human Gut ◽

Thai Population ◽

Shotgun Metagenomics ◽

Human Gut Microbiome ◽

Metabolic Functions

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

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Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.728479 ◽

2021 ◽

Vol 12 ◽

Author(s):

Liangwei Mao ◽

Yu Zhang ◽

Jing Tian ◽

Ming Sang ◽

Guimin Zhang ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Gut Microbiome ◽

Clinical Symptoms ◽

Characteristic Curve ◽

Central China ◽

Metagenomic Sequencing ◽

Microbial Composition ◽

Protein Database ◽

Shotgun Metagenomics

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.

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Ecological and Evolutionary Alterations in Graves’ Disease Gut Microbiome Reveal Specific Diagnostic Biomarkers

10.21203/rs.3.rs-113330/v1 ◽

2020 ◽

Author(s):

Qiyun Zhu ◽

Qiangchuan Hou ◽

Shi Huang ◽

Qianying Ou ◽

Yoshiki Vázquez-Baeza ◽

...

Keyword(s):

Gut Microbiome ◽

Small Sample Size ◽

Meta Analysis ◽

Small Sample ◽

Classification Model ◽

Graves Disease ◽

Metagenomic Sequencing ◽

Pilot Studies ◽

Shotgun Metagenomics ◽

Microbial Biomarkers

Abstract Background: Graves’ Disease (GD) is the most common organ-specific autoimmune disease and has been linked in small pilot studies to taxonomic markers within the gut microbiome. However, the small sample size and limited resolution of the 16S rRNA amplicon sequencing technology limited the universality and significance of these studies. Larger cohorts and integration of different levels of analysis from high-resolution shotgun metagenomics data were therefore needed to explore the GD patients’ alteration in gut microbial taxonomy, genes, pathways and functions, metabolites, and mutational spectra, to establish robust microbial biomarkers at these levels for GD diagnosis.Results: Here, we studied 162 gut microbiomes of mild and severe Graves’ disease (GD) patients and healthy controls. Shotgun metagenomic sequencing and inferred metabolomics were applied to describe the intestinal microbial characteristics and microbial mutations of GD patients. Then, combined biomarkers were identified from machine learning. Finally, we performed a meta-analysis to confirm the specificity of these biomarkers across different metabolic and autoimmune diseases. Taxonomic and functional analyses based on metagenome-assembled genomes (MAGs) and MAG-annotated genes, together with predicted metabolic functions and metabolite profiles, revealed a bipartite co-occurrence network of MAGs, genes and clinical indexes separating healthy from GD subjects. A supervised classification model identified a combination of biomarkers including microbial species, MAGs, genes and SNPs, with predictive power superior to models from any single biomarker type (AUC=0.98). Global, cross-disease meta-analysis of gut microbiomes revealed high specificity of these GD biomarkers, notably discriminating against Parkinson’s Disease, and suggesting that non-invasive stool-based diagnostics will be useful for these diseases.Conclusions: This work extended our understanding of the microbial ecology and evolution of GD pathogenesis, and developed a useful predictive model for GD diagnosis based on intestinal microbial biomarkers.

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#85: Nutrient Availability Drives Community Dynamics in the Vaginal Microbiota

Journal of the Pediatric Infectious Diseases Society ◽

10.1093/jpids/piaa170.027 ◽

2021 ◽

Vol 10 (Supplement_1) ◽

pp. S9-S9

Author(s):

M Indriati Hood-Pishchany ◽

Seth Rakoff-Nahoum

Keyword(s):

Community Dynamics ◽

Bacterial Species ◽

Nutrient Utilization ◽

Strain Level ◽

In Vitro Cultivation ◽

Carbohydrate Utilization ◽

Glycogen Utilization ◽

The Impact

Abstract Background Nutrient utilization is both critical for niche occupation and is the driver of competitive and cooperative interactions in microbial communities. The FRT is replete with host-associated glycans in the form of glycoproteins, epithelial glycogen stores, and the breakdown products of these glycans. I hypothesized that host-associated glycans drive environment, microbe–microbe and host–microbe interactions in the FRT. Methods We have developed robust, scalable, high-throughput culturing systems to empirically define the substrate utilization traits from more than 60 unique bacterial species capable of colonizing the vagina. In addition, we are using batch and continuous culture in vitro cultivation of multispecies communities to study vaginal bacteria within the complex community, that closely recapitulate key dynamics observed in vivo. Results Demonstrating the power of these in vitro models, I have defined the carbohydrate utilization profiles of hundreds of unique FRT isolates, identifying species and strain-level variation in utilization of host-derived carbohydrates. Given the known abundance of glycogen in the vaginal epithelium, I hypothesized that the utilization of host-associated glycogen represents an adaptation to the vaginal environment. Indeed, we identify glycogen degradation enzymes in diverse species resident in the reproductive tract, and find enrichment in genes encoding glycogen-degrading enzymes in L. crispatus strains derived from vaginal as opposed to intestinal sites. Metatranscriptomic analyses from human samples demonstrate that bacterial glycogen and maltose (a breakdown product of glycogen) utilization genes are highly expressed in the vagina and elucidate patterns of gene expression suggestive of context-dependent competition and cooperation for glycogen utilization in vivo. To empirically investigate the impact of glycogen availability and glycogen utilization in FRT microbiota communities, I assembled type strains or co-resident consortia into model, polymicrobial communities in vitro. These studies demonstrate that among health-associated L. crispatus strains, those that use glycogen have a competitive advantage during growth in a complex community. However, preliminary results suggest that some strains may benefit from cross-fed nutrients liberated by other members of the consortium. Conclusions Taken together, these data establish that strain-level variability in glycan utilization contributes to competitive fitness during growth in community, and suggest that these traits may influence community stability or persistence in vivo. Moreover, the methods we have developed provide a scalable system in which to empirically study ecological dynamics within complex community ex vivo.

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