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1. Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter

   https://doi.org/10.1128/spectrum.01067-22  

   Catlett, Jennie L. ; Carr, Sean ; Cashman, Mikaela ; Smith, Megan D. ; Walter, Mary ; Sakkaff, Zahmeeth ; Kelley, Christine ; Pierobon, Massimiliano ; Cohen, Myra B. ; Buan, Nicole R. ( June 2022 , Microbiology Spectrum)

   Claesen, Jan (Ed.)

   ABSTRACT Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii , are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron . To study their metabolic interactions, we defined and optimized a coculture system and used software testing techniques to analyze growth under a range of conditions representing the nutrient environment of the host. We verify that B. thetaiotaomicron fermentation products are sufficient for M. smithii growth and that accumulation of fermentation products alters secretion of metabolites by B. thetaiotaomicron to benefit M. smithii . Studies suggest that B. thetaiotaomicron metabolic efficiency is greater in the absence of fermentation products or in the presence of M. smithii . Under certain conditions, B. thetaiotaomicron and M. smithii form interspecies granules consistent with behavior observed for syntrophic partnerships between microbes in soil or sediment enrichments and anaerobic digesters. Furthermore, whenmore »vitamin B 12 , hematin, and hydrogen gas are abundant, coculture growth is greater than the sum of growth observed for monocultures, suggesting that both organisms benefit from a synergistic mutual metabolic relationship. IMPORTANCE The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions. We studied the interactions between two dominant human gut microbes, B. thetaiotaomicron and M. smithii , using a seven-component culturing approach that allows the systematic examination of the metabolic complexity of this binary microbial system. By combining high-throughput methods with machine learning techniques, we were able to investigate the interactions between two dominant genera of the gut microbiome in a wide variety of environmental conditions. Our approach can be broadly applied to studying microbial interactions and may be extended to evaluate and curate computational metabolic models. The software tools developed for this study are available as user-friendly tutorials in the Department of Energy KBase.« less
2. Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer

   https://doi.org/10.1128/spectrum.00013-22  

   Avuthu, Nagavardhini ; Guda, Chittibabu ( June 2022 , Microbiology Spectrum)

   Claesen, Jan (Ed.)

   ABSTRACT Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. The dysbiotic gut microbiota and its metabolite secretions play a significant role in CRC development and progression. In this study, we identified microbial and metabolic biomarkers applicable to CRC using a meta-analysis of metagenomic datasets from diverse geographical regions. We used LEfSe, random forest (RF), and co-occurrence network methods to identify microbial biomarkers. Geographic dataset-specific markers were identified and evaluated using area under the ROC curve (AUC) scores and random effect size. Co-occurrence networks analysis showed a reduction in the overall microbial associations and the presence of oral pathogenic microbial clusters in CRC networks. Analysis of predicted metabolites from CRC datasets showed the enrichment of amino acids, cadaverine, and creatine in CRC, which were positively correlated with CRC-associated microbes ( Peptostreptococcus stomatis , Gemella morbillorum , Bacteroides fragilis , Parvimonas spp., Fusobacterium nucleatum , Solobacterium moorei , and Clostridium symbiosum ), and negatively correlated with control-associated microbes. Conversely, butyrate, nicotinamide, choline, tryptophan, and 2-hydroxybutanoic acid showed positive correlations with control-associated microbes ( P < 0.05). Overall, our study identified a set of global CRC biomarkers that are reproducible across geographic regions. We also reported significant differential metabolitesmore »and microbe-metabolite interactions associated with CRC. This study provided significant insights for further investigations leading to the development of noninvasive CRC diagnostic tools and therapeutic interventions. IMPORTANCE Several studies showed associations between gut dysbiosis and CRC. Yet, the results are not conclusive due to cohort-specific associations that are influenced by genomic, dietary, and environmental stimuli and associated reproducibility issues with various analysis approaches. Emerging evidence suggests the role of microbial metabolites in modulating host inflammation and DNA damage in CRC. However, the experimental validations have been hindered by cost, resources, and cumbersome technical expertise required for metabolomic investigations. In this study, we performed a meta-analysis of CRC microbiota data from diverse geographical regions using multiple methods to achieve reproducible results. We used a computational approach to predict the metabolomic profiles using existing CRC metagenomic datasets. We identified a reliable set of CRC-specific biomarkers from this analysis, including microbial and metabolite markers. In addition, we revealed significant microbe-metabolite associations through correlation analysis and microbial gene families associated with dysregulated metabolic pathways in CRC, which are essential in understanding the vastly sporadic nature of CRC development and progression.« less
3. Symbiont Genomic Features and Localization in the Bean Beetle Callosobruchus maculatus

   https://doi.org/10.1128/AEM.00212-21  

   Berasategui, Aileen ; Moller, Abraham G. ; Weiss, Benjamin ; Beck, Christopher W. ; Bauchiero, Caroline ; Read, Timothy D. ; Gerardo, Nicole M. ; Salem, Hassan ( May 2021 , Applied and Environmental Microbiology)

   Johnson, Karyn N. (Ed.)

   ABSTRACT A pervasive pest of stored leguminous products, the bean beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) associates with a simple bacterial community during adulthood. Despite its economic importance, little is known about the compositional stability, heritability, localization, and metabolic potential of the bacterial symbionts of C. maculatus . In this study, we applied community profiling using 16S rRNA gene sequencing to reveal a highly conserved bacterial assembly shared between larvae and adults. Dominated by Firmicutes and Proteobacteria , this community is localized extracellularly along the epithelial lining of the bean beetle’s digestive tract. Our analysis revealed that only one species, Staphylococcus gallinarum (phylum Firmicutes ), is shared across all developmental stages. Isolation and whole-genome sequencing of S. gallinarum from the beetle gut yielded a circular chromosome (2.8 Mb) and one plasmid (45 kb). The strain encodes complete biosynthetic pathways for the production of B vitamins and amino acids, including tyrosine, which is increasingly recognized as an important symbiont-supplemented precursor for cuticle biosynthesis in beetles. A carbohydrate-active enzyme search revealed that the genome codes for a number of digestive enzymes, reflecting the nutritional ecology of C. maculatus . The ontogenic conservation of the gut microbiota in the bean beetle, featuring a “core” community composedmore »of S. gallinarum , may be indicative of an adaptive role for the host. In clarifying symbiont localization and metabolic potential, we further our understanding and study of a costly pest of stored products. IMPORTANCE From supplementing essential nutrients to detoxifying plant secondary metabolites and insecticides, bacterial symbionts are a key source of adaptations for herbivorous insect pests. Despite the pervasiveness and geographical range of the bean beetle Callosobruchus maculatus , the role of microbial symbioses in its natural history remains understudied. Here, we demonstrate that the bean beetle harbors a simple gut bacterial community that is stable throughout development. This community localizes along the insect’s digestive tract and is largely dominated by Staphylococcus gallinarum . In elucidating symbiont metabolic potential, we highlight its possible adaptive significance for a widespread agricultural pest.« less
4. Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

   https://doi.org/10.1186/s40168-020-00975-x  

   Klassen, Leeann ; Reintjes, Greta ; Tingley, Jeffrey P. ; Jones, Darryl R. ; Hehemann, Jan-Hendrik ; Smith, Adam D. ; Schwinghamer, Timothy D. ; Arnosti, Carol ; Jin, Long ; Alexander, Trevor W. ; et al ( December 2021 , Microbiome)

   Abstract Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as “medium grower” and “high grower.” Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and “omics” approaches tomore »characterize microbial adaptation to a prebiotic in the rumen ecosystem.« less
5. Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism

   https://doi.org/10.1038/s41396-021-01136-0  

   Carrell, Alyssa A. ; Veličković, Dušan ; Lawrence, Travis J. ; Bowen, Benjamin P. ; Louie, Katherine B. ; Carper, Dana L. ; Chu, Rosalie K. ; Mitchell, Hugh D. ; Orr, Galya ; Markillie, Lye Meng ; et al ( November 2021 , The ISME Journal)

   Interactions betweenSphagnum(peat moss) and cyanobacteria play critical roles in terrestrial carbon and nitrogen cycling processes. Knowledge of the metabolites exchanged, the physiological processes involved, and the environmental conditions allowing the formation of symbiosis is important for a better understanding of the mechanisms underlying these interactions. In this study, we used a cross-feeding approach with spatially resolved metabolite profiling and metatranscriptomics to characterize the symbiosis betweenSphagnumandNostoccyanobacteria. A pH gradient study revealed that theSphagnum–Nostocsymbiosis was driven by pH, with mutualism occurring only at low pH. Metabolic cross-feeding studies along with spatially resolved matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) identified trehalose as the main carbohydrate source released bySphagnum, which were depleted byNostocalong with sulfur-containing choline-O-sulfate, taurine and sulfoacetate. In exchange,Nostocincreased exudation of purines and amino acids. Metatranscriptome analysis indicated thatSphagnumhost defense was downregulated when in direct contact with theNostocsymbiont, but not as a result of chemical contact alone. The observations in this study elucidated environmental, metabolic, and physiological underpinnings of the widespread plant–cyanobacterial symbioses with important implications for predicting carbon and nitrogen cycling in peatland ecosystems as well as the basis of general host-microbe interactions.