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  • Springer Nature  (5)
  • 2020-2024  (5)
  • 1
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    Metabolic independence drives gut microbial colonization and resilience in health and disease (2023)
    Springer Nature
    In:  EPIC3Genome Biology, Springer Nature, 24(1), pp. 78-78, ISSN: 1474-760X
    Details
    Publication Date: 2024-04-03
    Description: Background: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Results: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. Conclusions: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 2
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    Microbial metabolites in the marine carbon cycle (2022)
    Springer Nature
    In:  EPIC3Nature Microbiology, Springer Nature, 7(4), pp. 508-523, ISSN: 2058-5276
    Details
    Publication Date: 2024-04-03
    Description: One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 3
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    Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess (2024)
    Springer Nature
    In:  EPIC3Nature Microbiology, Springer Nature, 9(3), pp. 830-847, ISSN: 2058-5276
    Details
    Publication Date: 2024-04-03
    Description: Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive ‘plasmid systems’ using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 4
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    Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration (2024)
    Springer Nature
    In:  EPIC3Nature Microbiology, Springer Nature, 9(1), pp. 55-69, ISSN: 2058-5276
    Details
    Publication Date: 2024-04-03
    Description: Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme–substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 5
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    Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples (2023)
    Springer Nature
    In:  EPIC3Nature Methods, Springer Nature, 20(11), pp. 1672-1682, ISSN: 1548-7091
    Details
    Publication Date: 2024-04-03
    Description: Host–microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host–microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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