Dissecting the in Vivo Metabolic Potential of Two Human Gut Acetogens

Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
Journal of Biological Chemistry (Impact Factor: 4.57). 05/2010; 285(29):22082-90. DOI: 10.1074/jbc.M110.117713
Source: PubMed


Fermenting microbial communities generate hydrogen; its removal through the production of acetate, methane, or hydrogen sulfide
modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components
for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers
than components for methanogenesis or sulfate reduction and subsequently analyzed the metabolic potential of two sequenced
human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally
applicable method for multiplex sequencing of expressed microbial mRNAs (microbial RNA-Seq) and, together with mass spectrometry
of metabolites, showed that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents,
thereby maintaining a high NAD+/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings
have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that
modulate energy harvest.

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    • "Members of this phylum generally act as mutualists by aiding in the digestion of complex carbohydrates, promoting gut development , modulating the immune system, and protecting against colonization by pathogens (Round and Mazmanian, 2009; Smith et al., 2006; Thomas et al., 2011). As metabolically pliable organisms, Bacteroidetes also help to support a diverse gut community through syntrophic interactions with other microbes (Fischbach and Sonnenburg, 2011; Rey et al., 2010). Evidence suggests that the capacity of a bacterium to survive in a polymicrobial environment is related to the elaboration of interbacterial antagonistic factors. "
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    ABSTRACT: Bacteroidetes are a phylum of Gram-negative bacteria abundant in mammalian-associated polymicrobial communities, where they impact digestion, immunity, and resistance to infection. Despite the extensive competition at high cell density that occurs in these settings, cell contact-dependent mechanisms of interbacterial antagonism, such as the type VI secretion system (T6SS), have not been defined in this group of organisms. Herein we report the bioinformatic and functional characterization of a T6SS-like pathway in diverse Bacteroidetes. Using prominent human gut commensal and soil-associated species, we demonstrate that these systems localize dynamically within the cell, export antibacterial proteins, and target competitor bacteria. The Bacteroidetes system is a distinct pathway with marked differences in gene content and high evolutionary divergence from the canonical T6S pathway. Our findings offer a potential molecular explanation for the abundance of Bacteroidetes in polymicrobial environments, the observed stability of Bacteroidetes in healthy humans, and the barrier presented by the microbiota against pathogens.
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    • "A strain's abundance is not the ideal proxy for its importance; low-abundance members of a community can play key and very diverse roles in community function and host biology [34], [35]. Indeed, we could find strains that had a consistently low abundance across most of the sample set, indicating that they might play an important role in community function despite their low numbers (Figure S10A–C). "
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    ABSTRACT: Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.
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    • "Hydrogen and carbon dioxide are produced as a byproduct of fermentation by both NM10 and BL7 using both glucose and lactate as substrates (Figure 8). Hydrogen and carbon dioxide produced during fermentation are utilized by methanogens, while hydrogen is utilized by acetogens and sulphate-reducing bacteria as a substrate for metabolism [61]–[63]. This makes Megasphaera sp. an important part of the food chain in the human gut environment. "
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    ABSTRACT: With increasing number of novel bacteria being isolated from the human gut ecosystem, there is a greater need to study their role in the gut ecosystem and their effect on the host health. In the present study, we carried out in silico genome-wide analysis of two novel Megasphaera sp. isolates NM10 (DSM25563) and BL7 (DSM25562), isolated from feces of two healthy individuals and validated the key features by in vitro studies. The analysis revealed the general metabolic potential, adaptive features and the potential effects of these isolates on the host. The comparative genome analysis of the two human gut isolates NM10 and BL7 with ruminal isolate Megasphaera elsdenii (DSM20460) highlighted the differential adaptive features for their survival in human gut. The key findings include features like bile resistance, presence of various sensory and regulatory systems, stress response systems, membrane transporters and resistance to antibiotics. Comparison of the "glycobiome" based on the genomes of the ruminal isolate with the human gut isolates NM10 and BL revealed the presence of diverse and unique sets of Carbohydrate-Active enzymes (CAZymes) amongst these isolates, with a higher collection of CAZymes in the human gut isolates. This could be attributed to the difference in host diet and thereby the environment, consequently suggesting host specific adaptation in these isolates. In silico analysis of metabolic potential predicted the ability of these isolates to produce important metabolites like short chain fatty acids (butyrate, acetate, formate, and caproate), vitamins and essential amino acids, which was further validated by in vitro experiments. The ability of these isolates to produce important metabolites advocates for a potential healthy influence on the host. Further in vivo studies including transcriptomic and proteomic analysis will be required for better understanding the role and impact of these Megasphaera sp. isolates NM10 and BL7 on the human host.
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