Biology subjects

Ley, R. E.

Publications and source records attributed to Ley, R. E..

35 records · Page 2Linked to original sources

bioRxiv2020

Strong influence of vertebrate host phylogeny on gut archaeal diversity

Commonly used 16S rRNA gene primers miss much of the archaeal diversity present in the vertebrate gut, leaving open the question of which archaea are host associated, the specificities of such associations, and the major factors influencing archaeal diversity. We applied 16S rRNA amplicon sequencing with Archaea-targeting primers to a dataset of 311 fecal/gut samples spanning 5 taxonomic classes (Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii) and obtained from mainly wild individuals (76% were wild). We obtained sufficient archaeal sequence data from 185 samples comprising 110 species that span all 5 classes. We provide evidence for novel Archaea-host associations, including Bathyarchaeia and Methanothermobacter -- the latter of which was prevalent among Aves and enriched in higher body temperatures. Host phylogeny more strongly explained archaeal diversity than diet, while specific taxa were associated with each factor. Co-phylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last command ancestors of mammals and all host species. Archaea-Bacteria interactions seem to have a limited effect on archaeal diversity. These findings substantially expand on the paradigm of Archaea-vertebrate associations and the factors that explain those associations. SignificanceArchaea play key roles in the vertebrate gut such as promoting bacterial fermentation via consumption of waste products. Moreover, gut-inhabiting methanogenic Archaea in livestock are a substantial source of greenhouse gas production. Still, much is not known of the archaeal diversity in most vertebrates, especially since 16S rRNA sequence surveys often miss much of the archaeal diversity that is present. By applying Archaea-targeted gut microbiome sequencing to a large collection of diverse vertebrates, we reveal new Archaea-host associations such as a high prevalence of Methanothermobacter in birds. We also show that host evolutionary history explains archaeal diversity better than diet, and certain genera in one particular class of Archaea (Methanobacteria) were likely pervasive in the ancestral vertebrate gut.

microbiology↗

bioRxiv2020

Free-living psychrophilic bacteria of the genus Psychrobacter are descendents of pathobionts

Host-adapted microbiota are generally thought to have evolved from free-living ancestors. This process is in principle reversible, but examples are few. The genus Psychrobacter (family Moraxellaceae, phylum Gamma-Proteobacteria) includes species inhabiting diverse and mostly polar environments, such as sea ice and marine animals. To probe Psychrobacters evolutionary history, we analyzed 85 Psychrobacter strains by comparative genomics and phenotyping under 24 different growth conditions. Genome-based phylogeny shows Psychrobacter are derived from Moraxella, which are warm-adapted pathobionts. Psychrobacter strains form two ecotypes based on growth temperature: flexible (FE, growth at 4 - 37{degrees}C), and restricted (RE, 4 - 25{degrees}C). FE strains, which can be either phylogenetically basal or derived, have smaller genomes and higher transposon copy numbers. RE strains have larger genomes, and show genomic adaptations towards a psychrophilic lifestyle and are phylogenetically derived only. We then assessed Psychrobacter abundance in 86 mostly wild polar bear stools and tested persistence of select strains in germfree mice. Psychrobacter (both FE and RE) was enriched in stool of polar bears feeding on mammals, but only FE strains persisted in germfree mice. Together these results indicate growth at 37{degrees}C is ancestral in Psychrobacter, lost in many derived species, and likely necessary to colonize the mammalian gut.

microbiology↗

bioRxiv2020

Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb.nov. based on whole genome analysis

The genera Catabacter (family Catabacteraceae) and Christensenella (family Christensenellaceae) are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore forming, short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis. A concatenated alignment of 135 shared protein sequences indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the new genus as Christensenella hongkongensis comb.nov.

microbiology↗

bioRxiv2020

Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut

Archaea of the order Methanomassiliicoccales use methylated-amines such as trimethylamine as a substrate for methane production. They form two large phylogenetic clades and reside in diverse environments, from soil to the human gut. Two genera, one from each clade, inhabit the human gut: Methanomassiliicoccus, which has one cultured representative, and "candidatus Methanomethylophilus", which has none. Questions remain regarding their distribution across different biomes and human populations, their association with other taxa in the human gut, and whether host genetics correlate with their abundance. To gain insight into the Methanomassiliicoccales, and the human-associated members in particular, we performed a genomic comparison of 72 Methanomassiliicoccales genomes and assessed their presence in metagenomes derived from the human gut (n=4472 representing 25 populations), nonhuman animal gut (n=145) and nonhost environments (n=160). Our analyses showed that all taxa are generalists: they were detected in animal gut and environmental samples. We confirmed two large clades, one enriched in the gut, the other enriched in the environment, with notable exceptions. Genomic adaptations to the gut include genome reduction, a set of adhesion factors distinct from that of environmental taxa, and genes involved in the shikimate pathway and bile resistance. Genomic adaptations differed by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, the relative abundance of Methanomassiliicoccales correlated with trimethylamine-producing bacteria and was unrelated to host genotype. Our results shed light on the microbial ecology of this group may help guide Methanomassiliicoccales-based strategies for trimethylamine mitigation in cardiovascular disease. ImportanceMethanomassiliicoccales are a lesser known component of the human gut microbiota. This archaeal order is composed of methane producers that use methylated amines, such as trimethylamine, in methane production. This group has only one cultured representative; how they adapted to inhabit the mammalian gut and how they interact with other microbes is largely unknown. Using bioinformatics methods applied to DNA from a wide range of samples, we profiled the relative abundances of these archaea in environmental and host-associated microbial communities. We observed two groups of Methanomassiliicoccales, one largely host-associated and one largely found in environmental samples, with some exceptions. When host-associated, these archaea have a distinct set of genes related to adhesion and possess genes related to bile resistance. We did not detect Methanomassiliicoccales in all human populations tested but when present, they are correlated with Bacteria known to produce trimethylamine. Since trimethylamine is linked to cardiovascular disease risk, these intriguing Archaea may also be involved.

microbiology↗

bioRxiv2020

The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil

Studies in mice using germfree animals as controls for microbial colonization have shown that the gut microbiome mediates diet-induced obesity. Such studies use diets rich in saturated fat, however, Western diets in the USA are enriched in soybean oil, composed of unsaturated fatty acids (FAs), either linoleic or oleic acid. Here we addressed whether the microbiome is a variable in fat metabolism in mice on a soybean oil diet. We used conventionally-raised, low-germ, and germfree mice fed for 10 weeks diets either high (HF) or low (LF) in high-linoleic-acid soybean oil as the sole source of fat. All mice, including germfree, gained relative fat weight and consumed more calories on the HF versus LF soybean oil diet. Plasma fatty acid levels were generally dependent on diet, with microbial colonization status affecting iso-C18:0, C20:3n-6, C14:0, and C15:0 levels. Colonization status, but not diet, impacted levels of liver sphingolipids including ceramides, sphingomyelins, and sphinganine. Our results confirm that absorbed fatty acids are mainly a reflection of the diet, and show that microbial colonization influences liver sphingolipid pools.

systems biology↗

bioRxiv2020

Incorporating genome-based phylogeny and trait similarity into diversity assessments helps to resolve a global collection of human gut metagenomes

Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). The Genome Taxonomy Database (GTDB) provides a genome-based reference database that can be used for species-level metagenome profiling, and a multi-locus phylogeny of all genomes that can be employed for diversity calculations. This approach also allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 33 studies and 3348 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or on par with tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Notably, ecophylogenetic and functional diversity measures were generally the most important features for predictive performance. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity - a fundamental component of microbiome science. ImportanceEstimations of microbiome diversity are fundamental to understanding spatiotemporal changes of microbial communities and identifying which factors mediate such changes. Tree-based measures of diversity, which consider species relatedness, are widespread for amplicon-based microbiome studies due to their utility relative to tree-agnostic measures. However, tree-based measures are seldomly applied to shotgun metagenomics data. We evaluated the utility of phylogeny, functional relatedness, and tree-agnostic diversity measures on a large scale human gut metagenome dataset to help guide researchers with the complex task of evaluating microbiome diversity via metagenomics.

bioinformatics↗

bioRxiv2020

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 5596 metagenome-assembled genomes from the gut metagenomes of 180 predominantly wild animal species representing 5 classes, in addition to 14 existing animal gut metagenome datasets. The MAGs comprised 1522 species-level genome bins (SGBs); most of which were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1986 diverse biosynthetic gene clusters; only 23 clustered with any MIBiG database references. Gene-based assembly revealed tremendous gene diversity, much of it host- or environment-specific. Our MAG and gene datasets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to the vertebrate gut. ImportanceMicrobiome studies on a select few mammalian species (e.g., humans, mice, and cattle) have revealed a great deal of novel genomic diversity in the gut microbiome. However, little is known of the microbial diversity in the gut of other vertebrates. We studied the gut microbiome of a large set of mostly wild animal species consisting of mammals, birds, reptiles, amphibians, and fish. Unfortunately, we found that existing reference databases commonly used for metagenomic analyses failed to capture the microbiome diversity among vertebrates. To increase database representation, we applied advanced metagenome assembly methods to our animal gut data and to many public gut metagenome datasets that had not been used to obtain microbial genomes. Our resulting genome and gene cluster collections comprised a great deal of novel taxonomic and genomic diversity, which we extensively characterized. Our findings substantially expand what is known of microbial genomic diversity in the vertebrate gut.

microbiology↗

bioRxiv2019

Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut

Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae co-occur and are enriched in individuals with a lean, compared to an obese, BMI. Whether these association patterns reflect interactions between metabolic partners remains to be ascertained, as well as whether these associations play a role in the lean host phenotype with which they associate. Here, we validated previously reported co-occurrence patterns of the two families, and their association with a lean BMI, with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species level between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By co-culturing three Christensenella spp. With M. smithii, we show that Christensenella spp. efficiently support the of M. smithii via H2 production, far better than Bacteroides thetaiotaomicron. C. minuta forms flocs colonized by M. smithii even when H2 is in excess. In culture with C. minuta, H2 consumption by M. smithii shifts the metabolic output of C. minutas fermentation towards acetate rather than butyrate. Together, these results indicate that the widespread co-occurrence of these microbiota is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI. ImportanceThe human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea. The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact, and how they affect the body type, are unanswered questions. Here, we showed that species within these families correlate with each other across people. We also demonstrated that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate when these species grow together, their products have the potential to affect the physiology of their human host.

microbiology↗

bioRxiv2019

Struo: a pipeline for building custom databases for common metagenome profilers

SummaryTaxonomic and functional information from microbial communities can be efficiently obtained by metagenome profiling, which requires databases of genes and genomes to which sequence reads are mapped. However, the databases that accompany metagenome profilers are not updated at a pace that matches the increase in available microbial genomes. To address this, we developed Struo, a modular pipeline that automatizes the acquisition of genomes from public repositories and the construction of custom databases for multiple metagenome profilers. The use of custom databases that broadly represent the known microbial diversity by incorporating novel genomes results in a substantial increase in mappability of reads in synthetic and real metagenome datasets.\n\nAvailability and implementationSource code available for download at https://github.com/leylabmpi/Struo. Custom GTDB databases available at http://ftp.tue.mpg.de/ebio/projects/struo/\n\nContactnicholas.youngblut@tuebingen.mpg.de

bioinformatics↗

bioRxiv2019

DeepMAsED: Evaluating the quality of metagenomic assemblies

Motivation/backgroundMethodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large scale metagenome assemblies.\n\nResultsWe present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates close to a 5% contig misassembly rate in two recent large-scale metagenome assembly publications.\n\nConclusionsDeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modelling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects.\n\nAvailabilityDeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED.

bioinformatics↗

bioRxiv2019

High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition

The composition of the gut microbiome is impacted by a complex array of factors, from nutrient composition and availability, to physical factors like temperature, pH, and flow rate, as well as interactions among the members of the microbial community. Many of these factors are affected by the host, raising the question of how host genetic variation impacts microbiome composition. Though human studies confirm this type of role for host genetics, its overall importance is still a subject of debate and remains difficult to study. The mouse model, by allowing the strict control of genetics, nutrition, and other environmental factors, has provided an excellent opportunity to extend this work, and the Diversity Outbred (DO) mice in particular present a chance to pinpoint host genetic variants that influence microbiome composition at different levels of generality. Here, we apply 16S rRNA gene sequencing to fecal samples of 247 DO male mice to estimate heritability and perform taxon-specific QTL mapping of microbial relative abundances revealing an increasingly heterogeneous picture of host function and microbial taxa at the host-microbiome interface. We present the first report of significant heritability of phylum Tenericutes in mice, and find novel QTL-spanning genes involved in antibacterial pathways, immune and inflammatory disease, and lipid metabolism.

genetics↗

bioRxiv2019

Sphingolipid production by gut Bacteroidetes regulates glucose homeostasis

Levels of Bacteroidetes in the gut microbiome are positively associated with insulin resistance (IR) in humans. Considering that IR is promoted by elevations in hepatic sphingolipids (SL), particularly ceramides, and that Bacteroidetes are the only microbiome phylum possessing genes encoding serine palmitoyltransferase (SPT), which mediates SL synthesis, we investigated a potential link between bacterial SL production, host SL metabolism, and IR. In vitro, bacterial SLs entered colonocytes and were metabolized into complex SL, including ceramides. In mice, administration of WT Bacteroides thetaiotaomicron, but not a SPT-deficient mutant, resulted in elevated levels of liver ceramides and reduced responsiveness to exogenously administered insulin. This work establishes bacterial SLs as a new class of microbiome-derived molecule capable of impacting host metabolism.\n\nOne Sentence SummarySL production by gut Bacteroidetes regulates liver ceramide levels and insulin sensitivity.

microbiology↗

bioRxiv2019

Age and sex-dependent patterns of gut microbial diversity in human adults

Gut microbial diversity changes throughout the human lifespan and is known to be affected by host sex. We investigated the association of age, sex and gut bacterial alpha diversity in three large cohorts of adults from four geographical regions: US and UK cohorts in the American Gut Project, and two independent cohorts of Colombians and Chinese. In three of the four cohorts, we observed a strong positive association between age and alpha diversity in young adults that plateaued after age 40. We also found pronounced sex-dependent differences in younger but not middle-aged adults, and women had higher alpha diversity than men. In contrast, no association of alpha diversity with age or sex was observed in the Chinese cohort. These associations were maintained after adjusting for cardiometabolic parameters in the Colombian cohort and antibiotic usage in the AGP cohort, suggesting that these factors do not affect the association of alpha diversity with age and sex. We also used a machine learning approach to predict individual age based on the gut microbiome. Consistent with our alpha diversity-based findings, women had significantly higher predicted age than men in the US and UK cohort, with a reduced difference above age 40. This was not observed in the Colombian cohort and only in the group of middle-age adults in the Chinese cohort. Together, our results provide new insights into the influence of age and sex on biodiversity of the human gut microbiota during adulthood while highlighting similarities and differences across diverse cohorts.

microbiology↗

bioRxiv2019

The virome in adult monozygotic twins with concordant or discordant gut microbiomes

The virome is one of the most variable components of the human gut microbiome. Within twin-pairs, viromes have been shown to be similar for infants but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the viromes vast diversity is unclear. Here, we examined the relationship between microbiome diversity and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles were unique to each subject, dominated by Caudovirales and Microviridae, and exhibited a small core that included crAssphage. Microbiome-discordant twins had more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns were driven by the bacteriophages, not eukaryotic viruses. These observations support a strong role of the microbiome in patterning the virome.

microbiology↗

bioRxiv2018

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Multiple factors modulate microbial community assembly in the gut, but the magnitude of each can vary substantially across studies. This may be in part due to a heavy reliance on captive animals, which can have very different gut microbiomes versus their wild counterparts. In order to better resolve the influence of evolution and diet on gut microbiome diversity, we generated a large and highly diverse animal distal gut 16S rRNA microbiome dataset, which comprises 80 % wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decoupled the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor explains different aspects of diversity. Moreover, we resolved particular microbial taxa associated with host phylogeny or diet, and we show that Mammalia have a stronger signal of cophylogeny versus non-mammalian hosts. Additionally, our results from ecophylogenetics and co-occurrence analyses suggest that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.

microbiology↗

bioRxiv2018

Human salivary amylase gene copy number impacts oral and gut microbiomes

Host genetic variation influences the composition of the human microbiome. While studies have focused on associations between the microbiome and single nucleotide polymorphisms in genes, their copy number (CN) can also vary. Here, in a study of human subjects including a 2-week standard diet, we relate oral and gut microbiome to CN at the AMY1 locus, which encodes the gene for salivary amylase, active in starch degradation. We show that although diet standardization drove gut microbiome convergence, AMY1-CN influenced oral and gut microbiome composition and function. The gut microbiomes of low-AMY1-CN subjects had an enhanced capacity for breakdown of complex carbohydrates. Those of high-AMY1 subjects were enriched in microbiota linked to resistant starch fermentation, had higher fecal SCFAs, and drove higher adiposity when transferred to germfree mice. Gut microbiota results were validated in a larger separate population. This study establishes AMY1-CN as a genetic factor patterning microbiome composition and function.

genetics↗

bioRxiv2017

Resilience mechanisms of small intestinal lactobacilli to the toxicity of soybean oil fatty acids

Over the past century, soybean oil (SBO) consumption in the United States increased dramatically. The main SBO fatty acid, linoleic acid (18:2), inhibits in vitro the growth of lactobacilli, beneficial members of the small intestinal microbiota. Human-associated lactobacilli have declined in prevalence in Western microbiomes, but how dietary changes may have impacted their ecology is unclear. Here, we compared the in vitro and in vivo effects of 18:2 on Lactobacillus reuteri and L. johnsonii. Directed evolution in vitro in both species led to strong 18:2 resistance with mutations in genes for lipid biosynthesis, acid stress, and the cell membrane or wall. Small-intestinal Lactobacillus populations in mice were unaffected by chronic and acute 18:2 exposure, yet harbored both 18:2- sensitive and resistant strains. This work shows that extant small intestinal lactobacilli are protected from toxic dietary components via the gut environment as well as their own capacity to evolve resistance.

microbiology↗