Mammalian gut metabolomes mirror microbiome composition and host phylogeny.

In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish.

The term core microbiome describes microbes that are consistently present in a particular habitat. If the conditions in that habitat are highly variable, core microbes may also be considered to be ecological generalists. However, little is known about whether metabolic competition and microbial interactions influence the ability of some microbes to persist in the core microbiome while others cannot. We investigated microbial communities at three sites in the guts of European seabass under four dietary conditions. We identified generalist core microbial populations in each gut site that are shared across fish, present under multiple diets and persistent over time. We found that core microbes tend to show synergistic growth in co-culture, and low levels of predicted and validated metabolic competition. Within core microbial species, we found high levels of intraspecific variability and strain-specific habitat specialization. Thus, both intraspecific variability and interspecific facilitation may contribute to the ecological stability of the animal core microbiome.

Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects.

Niche modification is a process whereby the activity of organisms modifies their local environment creating new niches for other organisms. This process can have a substantial role in community assembly of gut microbial ecosystems due to their vast and complex metabolic activities. We studied the postprandial diurnal community oscillatory patterns of the rumen microbiome and showed that metabolites produced by the rumen microbiome condition its environment and lead to dramatic diurnal changes in community composition and function. After feeding, microbiome composition undergoes considerable change in its phylogenetic breadth manifested as a significant 3-5-fold change in the relative abundance of methanogenic archaea and main bacterial taxa such as Prevotella, in a manner that was independent of individual host variation and diet. These changes in community composition were accompanied by changes in pH and methane partial pressure, suggesting a strong functional connection. Notably, cross-incubation experiments combining metabolites and organisms from different diurnal time points showed that the metabolites released by microbes are sufficient to reproduce changes in community function comparable to those observed in vivo. These findings highlight microbiome niche modification as a deterministic process that drives diurnal community assembly via environmental filtering.

Higher adaptive functioning and lower rate of psychotic comorbidity in married versus unmarried individuals with 22q11.2 deletion syndrome.

22q11.2 deletion syndrome (22q11.2DS) is a relatively common genetic disorder. Due to improvement in pediatric care, affected individuals live into adulthood, some of whom marry or have committed relationships, and reproduce. The current study aimed to identify the factors that discriminate between married and unmarried adults with 22q11.2DS. In the presents study, 90 adults with 22q11.2DS (48 men/42 women), aged 29.8 ± 10.3 years, were included in the analysis. Psychiatric comorbidities, IQ score, and adaptive functioning were assessed using gold-standard diagnostic tools. Demographic factors, marital status, and reproductive status were evaluated by self-reports. Of the sample 25 adults (27.7%) were married and 14 (56%) of those had children. Married, as compared to unmarried individuals, were older, had less psychotic comorbidities, showed higher adaptive functioning in all domains of the Vineland Adaptive Behavior Scale, and had higher rates of independent living and sustained employment. Unexpectedly, married individuals showed higher rates of mood disorders and full scale IQ scores did not discriminate between the groups. We propose that multiple factors are associated with marital status among individuals with 22q11.2DS. Identification of key personal, functional, and social characteristics of those who married and reproduced may help counseling health professionals and clinicians in advising affected individuals and their families.