Wu, D. G. | bioRxiv Science

bioRxiv2024

Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments

Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfishs MAGs were more specialized for the degradation of proteins. The invertivorous triggerfishs gut MAGs lacked many carbohydrate degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs. ImportanceThe benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their hosts diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but lack a comprehensive understanding of the genome-based metabolic capabilities of how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. Herbivorous fish harbored a functionally diverse microbes with plant matter degraders, while the piscivorous and invertivorous fish had microbes that were more specialized in protein degradation.

microbiology↗

bioRxiv2023

Bacterial hemophilin homologs and their specific type eleven secretor proteins have conserved roles in heme capture and are diversifying as a family

Cellular life relies on enzymes that require metal cofactors, which must be acquired from extracellular sources. Bacteria utilize surface and secreted proteins to acquire such valuable nutrients from their environment. These include the cargo proteins of the type eleven secretion system (T11SS), which have been connected to host specificity, metal homeostasis, and nutritional immunity evasion. This Sec-dependent, Gram-negative secretion system is encoded by organisms throughout the phylum Proteobacteria, including human pathogens Neisseria meningitidis, Proteus mirabilis, Acinetobacter baumannii, and Haemophilus influenzae. Experimentally verified T11SS-dependent cargo include host metal acquisition proteins transferrin binding protein B (TbpB) and lactoferrin binding protein B (LbpB), as well as the hemophilin homologs heme receptor protein C (HrpC) and hemophilin A (HphA), the complement immune evasion protein factor-H binding protein (fHbp), and the host symbiosis factor nematode intestinal localization protein C (NilC). Secretion of each of these cargo proteins relies on a specific T11SS. Here, we examined the specificity of T11SS systems for their cognate cargo proteins using taxonomically distributed homolog pairs of T11SS and hemophilin cargo and explore the ligand binding ability of those hemophilin homologs. Our comparative ligand binding analysis of four hemophilin family proteins identified previously unknown ligand binding diversity within this protein family, which informed our description of structural features that are likely to contribute to heme/porphyrin binding specificity. In vivo expression of hemophilin homologs revealed that each was secreted in a specific manner by its cognate T11SS protein. Furthermore, secretion assays of chimeric hemophilin proteins revealed that specificity is predominantly dictated by the C-terminal domain of the cognate cargo. Meanwhile, the N-terminal effector domains of these T11SS-dependent cargo proteins feature porphyrin binding pockets that drive ligand binding affinity and specificity. In light of these results, we have termed this N-terminal domain the hemophilin ligand binding domain (Hlb) after its first characterized representative.

microbiology↗