More Like this

1. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

   https://doi.org/10.1038/s41564-022-01266-x  

   Shaffer, Justin P. ; Nothias, Louis-Félix ; Thompson, Luke R. ; Sanders, Jon G. ; Salido, Rodolfo A. ; Couvillion, Sneha P. ; Brejnrod, Asker D. ; Lejzerowicz, Franck ; Haiminen, Niina ; Huang, Shi ; et al ( December 2022 , Nature Microbiology)

   Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment. 

   more » « less
2. Metabolomic profiling of stool of two‐year old children from the INSIGHT study reveals links between butyrate and child weight outcomes

   https://doi.org/10.1111/ijpo.12833  

   Nandy, Debmalya ; Craig, Sarah J. C. ; Cai, Jingwei ; Tian, Yuan ; Paul, Ian M. ; Savage, Jennifer S. ; Marini, Michele E. ; Hohman, Emily E. ; Reimherr, Matthew L. ; Patterson, Andrew D. ; et al ( July 2021 , Pediatric Obesity)

   Metabolomic analysis is commonly used to understand the biological underpinning of diseases such as obesity. However, our knowledge of gut metabolites related to weight outcomes in young children is currently limited.

   To (1) explore the relationships between metabolites and child weight outcomes, (2) determine the potential effect of covariates (e.g., child's diet, maternal health/habits during pregnancy, etc.) in the relationship between metabolites and child weight outcomes, and (3) explore the relationship between selected gut metabolites and gut microbiota abundance.

   Using¹H‐NMR, we quantified 30 metabolites from stool samples of 170 two‐year‐old children. To identify metabolites and covariates associated with children's weight outcomes (BMI [weight/height²], BMIz‐score [BMI adjusted for age and sex], and growth index [weight/height]), we analysed the¹H‐NMR data, along with 20 covariates recorded on children and mothers, using LASSO and best subset selection regression techniques. Previously characterized microbiota community information from the same stool samples was used to determine associations between selected gut metabolites and gut microbiota.

   At age 2 years, stool butyrate concentration had a significant positive association with child BMI (p‐value = 3.58 × 10^–4), BMIz‐score (p‐value = 3.47 × 10^–4), and growth index (p‐value = 7.73 × 10^–4). Covariates such as maternal smoking during pregnancy are important to consider. Butyrate concentration was positively associated with the abundance of the bacterial genusFaecalibacterium(p‐value = 9.61 × 10⁻³).

   Stool butyrate concentration is positively associated with increased child weight outcomes and should be investigated further as a factor affecting childhood obesity.

    

   more » « less
3. Gut microbiota contribute to variations in honey bee foraging intensity

   https://doi.org/10.1093/ismejo/wrae030  

   Vernier, Cassondra L ; Nguyen, Lan Anh ; Gernat, Tim ; Ahmed, Amy Cash ; Chen, Zhenqing ; Robinson, Gene E ( February 2024 , The ISME Journal)

   Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. Although many studies have reported that experimental disruptions to the gut microbial community result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, because of their simple gut microbiota and complex division of labor characterized by colony-level variation in behavioral phenotypes. Although previous studies report correlational differences in gut microbial community associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between European honey bees (Apis mellifera). We found that gut microbial community structure differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in gut microbial community composition were associated with task experience. Moreover, single-microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused effects on foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral trait variation.

    

   more » « less
4. Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

   https://doi.org/10.1186/s42523-022-00182-z  

   Sparagon, Wesley J. ; Gentry, Emily C. ; Minich, Jeremiah J. ; Vollbrecht, Lisa ; Laurens, Lieve M. ; Allen, Eric E. ; Sims, Neil A. ; Dorrestein, Pieter C. ; Kelly, Linda Wegley ; Nelson, Craig E. ( December 2022 , Animal Microbiome)

   Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus . Results Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish. 

   more » « less
5. Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua

   https://doi.org/10.1111/mec.15370  

   Kennedy, Susan R. ; Tsau, Sophia ; Gillespie, Rosemary ; Krehenwinkel, Henrik ( February 2020 , Molecular Ecology)

   Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spiderBadumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet‐driven. This assumption is supported by a feeding experiment, in which two types of prey—crickets and fruit flies—both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket‐derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey‐associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.

    

   more » « less