Animal microbiome最新文献

Background: The bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience.

Results: Using long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), the latter of which suggests involvement of Endozoicomonas in host 'sex-type' steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses.

Conclusions: This study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning.

Background: The ocular surface microbiota (OSM) is important for eye health, and variations in OSM composition have been associated with multiple diseases in humans. Studies of OSM-disease dynamics in humans are confounded by lifestyle factors. Animal models provide a complementary approach to understanding biological systems, free from many confounds of human studies. Here, we provide the first study of the OSM of rhesus macaques, a premier animal model for eye health and disease. We describe the taxonomy of the rhesus macaque OSM, and explore compositional correlations with age, sex, and living condition.

Methods: We analyzed eyelid and conjunctival microbiota swabs from 132 individual rhesus macaques (Macaca mulatta) (57 males, 75 females, 1-26 years old) from one captive and one free-ranging group using 16 S rRNA V3/V4 MiSeq sequencing. We investigated alpha diversity, beta diversity, and differential abundance.

Results: We found several similarities between the top Phyla and Genera of the rhesus macaque OSM and those reported in human literature. Significantly higher alpha diversity, which may reflect age-related ocular surface mucous membrane integrity and immune function, was present in younger individuals compared to older ones. Higher alpha diversity was also present in free-ranging rhesus macaques compared to ones in captivity, possibly related to differences in diet, exercise, and medical exposures between macaques in different living conditions. Beta diversity was most strongly influenced by individual identity, followed by living conditions. Sex did not correlate with any OSM variation.

Conclusions: In this study we describe the taxonomic composition of the rhesus macaque OSM, and identify significant differences in alpha and beta diversity according to individual nonhuman primate host variables and the surrounding environment. Our findings suggest composition of the nonhuman primate OSM is shaped by age-related physiology, individual identity, and external living conditions. Our results offer novel insights into an underexplored region of the primate microbiome and highlight the utility of rhesus macaques as a model system for investigating the links between the OSM, ocular health, and disease.

Background: Microbiota sequencing has emerged a powerful tool for advancing aquatic nutrition research. However, few studies have comprehensively investigated the host microbiota's response to trace minerals. This study examined the role of organic copper supplementation in promoting the health of farmed white shrimp (Penaeus vannamei) from a microbiota perspective.

Results: In an 8-week feeding trial, shrimp were fed diets supplemented with no copper, 30 mg/kg inorganic copper (CuSO₄·5H₂O) or organic copper (Cu-proteinate). The apparent digestibility coefficients of copper and zinc, along with carbon and nitrogen assimilation, were determined. The V3-V4 region of the 16S rRNA gene was sequenced from feeds, intestines, gills, and water samples. Shrimp that fed the organic copper diet demonstrated healthier physiological status, higher apparent digestibility coefficients of both copper and zinc, as well as greater accumulation of copper, zinc, carbon, and nitrogen. The organic copper group exhibited distinct microbial diversity and a more complex microbial co-occurrence network, characterized by enhanced natural connectivity and robustness. Keystone taxa, including Vibrio, Candidatus_Bacilloplasma, and Photobacterium, contributed to network stability. Taxa associated with nutrient metabolism, including Butyricicoccus, Lactobacillus, and genera in the family Lachnospiraceae, Prevotellaceae, Rikenellaceae and Ruminococcaceae, were significantly enriched, correlating well with improved nutritional profiles. In accordance, functional annotation revealed that the organic copper group exhibited higher abundances of functional modules associated with nutrient and energy metabolism such as carbon and nitrogen cycling. Furthermore, host-selective pressure shaped the unique microbiota composition in the intestine and gill, which differed from the surrounding water and water source, with the gill microbiota potentially serving as a transitional bridge shaping the intestinal microbiota.

Conclusions: More stable host microbiota, enriched nutrient-metabolizing taxa, and enhanced ecological cycling in this study provide a potential strategy for innovative aqua-feed development. Our findings offer novel microbiota-centric insights into the role of organic copper in healthy shrimp farming.

Amur ide (Leuciscus waleckii), which inhabits Lake Dali, a soda lake in Northeast China with extremely high alkalinity (~ 53.57 mmol/L) and pH value (~ 9.6), is considered to be an ideal model for elucidating alkaline adaption mechanisms. To uncover the molecular mechanisms underlying this adaptation, we conducted a comparative study between the alkaline water ecotype (JY) and freshwater ecotype (DY). Both groups were exposed to a gradient of NaHCO₃ stress levels (0, 10, 30, and 50 mmol/L), and their responses were systematically assessed through integrated multi-omics analyses alongside physiological assays. Our results revealed that under low and moderate alkaline stress (10 and 30 mmol/L), JY group significantly upregulated the gene anpep, facilitating the hydrolysis of cysteinyl-glycine to release L-cysteine, thereby enhancing antioxidant capacity. Under high stress conditions (50 mmol/L), JY further synergistically upregulated gpx to activated the glutathione peroxidase (GPx) pathway to eliminate excess ROS. In contrast, the DY group predominantly relied on upregulating chac1-mediated γ-glutamyltransferase activity to facilitate glutathione cycling. Notably, while cysteinyl-glycine content significantly increased in the alkaline water ecotype (JY) under moderate and high alkalinity stress (30 and 50 mmol/L), the expression of its upstream gene chac1 was significantly downregulated. This paradox suggests alternative sources or regulatory mechanisms for cysteinyl-glycine accumulation in JY. Microbial tracing analysis revealed a positive correlation between cysteinyl-glycine levels and the gut microbiota genus Stenotrophomonas in JY, whose relative abundance increased progressively with elevated alkalinity. It is speculated that Stenotrophomonas may modulate host glutathione metabolism by regulating cysteinyl-glycine levels, thereby facilitating alkaline adaptation.

Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity. We profiled the salmon gut microbiome across 540 salmon samples in differing conditions with a view to capture the genomic diversity that can be resolved from the salmon gut. The salmon were exposed to 3 different nutritional additives: seaweed, blue mussel protein and silaged blue mussel protein, including both pre-smolts (30-60 g salmon reared in freshwater) as well as post-smolts (300-600 g salmon reared in saltwater). Using genome-resolved metagenomics, we generated a catalogue of 11 species-level bacterial MAGs from 188 input metagenome assembled genomes, with 5 species not found in other catalogues. This highlights that our understanding of salmon gut microbial diversity is still incomplete. A prevalent bacterial genome annotated as Mycoplasmoidaceae is present in adult fish, and a comparison of functions revealed significant sub-species variation. Juvenile fish have a different microbial diversity, dominated by a species of Pseudomonas aeruginosa. We also present the first viral catalogue for salmon including prophage sequences which can be linked to the bacterial MAGs.