Gill health is a major issue in aquaculture and the role of the gill microbiome in salmonid gill health is a growing research topic. To establish the role of gill microbiota in salmonid health, it is essential to understand the importance of environmental factors and fish-associated factors in shaping the gill microbiome, while also including technical factors such as sampling method and DNA extraction methods. We addressed the relative contributions of each factor in a meta-analysis of all publicly available salmonid gill microbiome studies. We reanalyzed 20 studies containing 804 high-quality gill samples of Atlantic salmon, rainbow trout and Arctic charr to determine which factors significantly explained variation and which genera of microorganisms are associated with specific factors and followed this up with an analysis of 400 gill- and environmental samples to find gill-specific microbial signatures across studies. We found that study-specific factors are the largest explanatory factor, followed by rearing system and species, while no other factors were significant. Across studies, disease led to a significantly reduced microbial diversity. Finally, we find that salmonids share multiple core genera including beneficial nitrogen-cycle bacteria which were also widespread throughout all rearing systems. Our findings support the need for more standardized sampling and extraction methods, to minimize study-specific factors when looking for biomarkers of health or disease. However, we also show that despite most variation coming from study-specific effects, shared signatures for disease (a reduced microbial richness) and potential beneficial microorganisms can be found across salmonid gill microbiota.
Gut microbiota is widely recognized as an important contributor to phenotypic variation in many production traits in livestock. In addition to host genetic determination, maternal gut microbiota may be transmitted to offspring through nongenetic pathways. Such nongenetic transmission suggests the possibility of improving offspring production traits through direct selection of parental individuals based on their gut microbiota characteristics. However, the extent of nongenetic maternal transmission of gut microbiota and its persistence after weaning remain poorly understood. To address this gap, we cross-fostered 120 newborn rabbits from 20 does and compared the gut microbiota of all kits at weaning (35 days of age) and two weeks post-weaning. Based on variance component analyses, we found that nursing does explained substantial proportions of the phenotypic variation in four alpha diversity metrics of kits at weaning, ranging from 0.218 ± 0.106 for the Evenness index to 0.469 ± 0.126 for the number of observed features. The significant influence of nursing does was further supported by pairwise comparisons of beta diversity among four groups defined according to whether pairs of offspring shared the same biological and/or nursing doe, using Kruskal-Wallis tests followed by Dunn’s post hoc comparisons. In contrast, biological does had no significant effect on the gut microbiota composition of kits at weaning. After weaning, the influence of the nursing doe remained detectable although the estimated common litter environmental effects were generally reduced, whereas the estimated contribution of host additive genetic effects increased. This study provides direct evidence in rabbits that offspring gut microbiota is predominantly shaped by nongenetic maternal transmission, with these maternal influences persisting after weaning. The demonstrated transmissibility of maternal microbiota characteristics supports the potential application of microbiome-based selection strategies in livestock breeding.
The reproductive microbiota is important for host’s health and breeding success. Cetaceans (whales, dolphins, porpoises) are aquatic-obligate mammals inhabiting microbe-rich water environments, posing unique challenges for establishing and maintaining healthy microbiota. Limited research has explored cetacean reproductive microbiomes, with no studies characterizing mammary and placental microbiota within the infraorder. We used 16S rRNA metabarcoding of 272 samples to characterize the genital, mammary, gastrointestinal, and respiratory microbiomes of 60 common bottlenose dolphins (Tursiops truncatus) and 4 rough-toothed dolphins (Steno bredanensis) housed under human care, in addition to milk and placenta samples from one common bottlenose dolphin. Microbiome composition differed profoundly between the two dolphin species and across body sites. Reproductive microbiomes were lower in species richness compared to gastric and respiratory microbiomes. Body site patterns were relatively conserved within dolphin species, although genital microbiomes tended to cluster by facility and respiratory microbiome varied geographically. Dolphins housed together off contraceptives exhibited similar vaginal and penile microbiomes, suggesting bacteria exchange between the sexes through socio-sexual contact. Contraceptive intake did not alter vaginal, mammary, gastric, rectal, and respiratory microbial profiles. Dolphin mammary slit hosted a microbiome distinct from other body sites. Mammary and milk microbiomes were similar, indicating that dolphin mammary slit may play a role in milk colonization. Staphylococcus, Enterococcus, Streptococcus, and Corynebacterium were detected in the placenta and corresponding deceased neonate, yet absent in mother’s vagina and habitat water, suggesting vertical transmission of potential pathogens occurred during gestation. Our findings reveal novel species- and body site-specific microbiome patterns that shed light on the interplay between host biology, social behavior, and microbial communities in dolphins.
Bees often exhibit gut microbiome-defined enterotypes impacting their health and pollination services. Bumblebees, keystone pollinators in montane and agriculture ecosystems, face significant population declines might linked to gut parasites, pathogens, and antibiotic exposure; however, whether their enterotypes reflect these specific stressors remains uncharacterized. Here, we investigate the gut microbiomes of two bumblebee species belonging to the subgenus Pyrobombus, which are commonly infested by the gut parasite Crithidia bombi and other pathogens with samples over four years in Hengduan Mountains in China. Metagenomic analysis of 175 individuals identified four distinct enterotypes in both bumblebee species. Enterotype I (23
Lactoferrin is a natural iron-binding glycoprotein with barrier-protective, immunomodulatory, and antimicrobial activities, which is widely applied in human nutritional supplements and infant food additives. The present study aimed to evaluate the effects of dietary lactoferrin supplementation on immune parameters, intestinal barrier function, serum metabolome, and fecal microbiota in kittens. In this study, a total of 24 healthy kittens were divided into three groups and fed a commercial basal diet (CON) and the basal diet supplemented with 500 or 1000 mg/kg lactoferrin (L-LF or H-LF), respectively, for 42 days. Blood samples were collected on day 21 and 42 for measurement of immune and intestinal barrier markers. A repeated-measures mixed-effects model was used for data analysis. Serum and fecal samples were collected on day 42 for untargeted metabolomics and metagenomic analysis, respectively. Compared with CON, serum IgA level in the H-LF group was significantly higher on day 21 and day 42 (p < 0.05). The H-LF group showed higher serum IgM and lower IL-6 levels than CON on day 21, and both lactoferrin groups reduced IL-1β concentration on day 42 (p < 0.05), in contrast with the CON. Additionally, serum lipopolysaccharide and zonulin were decreased by H-LF relative to the CON on day 42 (p < 0.05). Untargeted metabolomics analysis revealed that lactoferrin altered serum metabolite profiles and increased levels of proline betaine, L-argininium(1+), and carnitine in H-LF (p < 0.05). Metagenomic analysis indicated that both L-LF and H-LF had a higher relative abundance of Bacteroidota but lower Escherichia coli than CON (p < 0.05). The H-LF group also increased the abundance of Prevotella, Bifidobacterium and Segatella copri in the feces of kittens (p < 0.05). Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of biosynthesis of secondary metabolites, biosynthesis of various nucleotide sugars, and sphingolipid metabolism were significantly enriched in kittens fed with H-LF (p < 0.05). Overall, dietary lactoferrin enhanced immune function, improved intestinal barrier integrity, and remodeled the gut microbiota of kittens, with the higher dose (1000 mg/kg) showing more pronounced benefits.
Mosquitoes are major vectors of infectious diseases, with their midgut microbiota playing a crucial role in host development, reproduction, and pathogen interactions. However, characterizing midgut microbial communities remains challenging because host DNA often dominates metagenomic libraries, reducing the resolution of bacterial community profiling and hindering the recovery of microbial genomes. To evaluate strategies for bacterial DNA enrichment in this context, we compared three DNA extraction protocols applied to pooled Aedes aegypti midguts: (i) the QIAGEN DNeasy Blood and Tissue kit without filtration (DNeasy NF), (ii) the same kit preceded by a 5 μm filtration step to reduce eukaryotic material (DNeasy F), and (iii) the QIAGEN QIAamp Microbiome kit, which combines differential host cell lysis and enzymatic DNA depletion. Each method was assessed using qPCR-based quantification of bacterial and host DNA, SSU rRNA-based taxonomic profiling of metagenomic reads, and Metagenome-Assembled Genomes (MAGs) reconstruction using advanced binning approaches. Our results show that while the Microbiome kit provided the highest bacterial enrichment and captured a large fraction (> 85
The gut microbiota is involved in host metabolism, immunity, and energy homeostasis. Stressors, such as diets and environments, can cause changes in microbial compositions and genomic variations. Here, we performed a population genomic analysis to reveal the genetic landscape of the pig gut microbiome and identified microbial single-nucleotide variants (SNVs) associated with host fatness traits. We characterized genomic variant features of gut microbiota across three pig populations having distinct genetics background and raised in dramatically different environments: wild boars (free-range and natural diets), Tibetan pigs (semi-free, high-altitude, and hypoxic environment), and Duroc pigs (intensive farming, and commercial diets). At the population level, gut microbiome of wild boars harbored the lowest SNV density, but the highest pN/pS ratios, in contrast to the elevated SNV density and recombination rates observed in Duroc and Tibetan pigs. Functional profiles of genes under selection in microbial genomes also differed across populations: purifying selected genes were enriched in the pathway of simple sugar metabolism in Duroc pigs, but secondary bile acid biosynthesis in wild boars, with Tibetan pigs exhibiting an intermediate pattern that included additional flavonoid metabolism pathways. Positively selected genes were involved in carbohydrate metabolism and proteolysis in Duroc pigs, adhesion in wild boars, and mucin-binding functions in Tibetan pigs. To further investigate whether microbial SNVs affected pig fatness traits, we performed an association analysis in well-phenotyped F6 pigs from a designed mosaic pig population. We identified 11 microbial SNVs in Lactobacillus amylovorus, Limosilactobacillus reuteri, Streptococcus faecavium, and CAG-177 sp003514385 that were significantly associated with pig fatness-related traits. These SNVs were predicted to be involved in energy metabolic enzymes and epigenetic modification. All associations were independent of bacterial abundance, highlighting the value of SNV-based analyses beyond traditional abundance approaches. Our findings revealed distinct genomic signatures of gut microbiota across three pig populations and established a framework for linking microbial genetic variation to host phenotypes, moving beyond taxonomic composition.
The gut microbiota is a critical factor influencing the health and productivity of sows, with implications for sustainable swine production. This study aimed to identify key factors shaping the sow gut microbiota across six European countries and characterize the composition of the core gut microbiota during late gestation and lactation. We identified two distinct sow gut core microbiotas at gestation and lactation shared across the six examined European countries comprising 50
Bacterial symbionts and their animal hosts differ in the strength and type of selection pressures that promote their evolution and, as some host traits are phylogenetically conserved, their symbiotic bacterial communities could also exhibit greater similarity than expected by chance; a pattern known as phylosymbiosis. This might result from differences in bacterial assemblages across species-specific habitats, and/or from natural selection favouring host traits that allow harbouring functional species-specific bacteria (functional phylosymbiosis). We explored these patterns in eight Bucerotiformes taxa, including hoopoes, woodhoopoes, and hornbills, of which hoopoes and woodhoopoes harbour antibiotic-producing symbionts in their uropygial gland. We characterised uropygial secretion bacterial communities using high-throughput 16S-rRNA gene sequencing and analysed its association with avian phylogeny. Furthermore, we quantified antimicrobial activity of bacterial isolates, and explored its relationship with host phylogenetic distances and bacterial community composition. We found a significant correlation between avian phylogeny and bacterial community dissimilarities, supporting phylosymbiosis. Moreover, antimicrobial activity was significantly predicted by bacterial community composition and the relative abundance of particular strains in hoopoes and woodhoopoes. These findings suggest that antimicrobial properties of symbionts could be responsible for the detected phylosymbiosis and that natural selection may favour uropygial gland features allowing hosts to harbour specific antimicrobial-producing symbionts.
In the context of the broad utilization of antibiotics in poultry breeding, an increasing number of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are accumulating in chicken feces, which presents a latent danger to workers’ health. However, few studies have explored the effect of chicken rearing on the microbial flora of workers. In this study, using metagenomic analysis techniques, a panoramic view of the intestinal microbiome and resistome across 40 chickens, 31 farm workers and 23 control villagers was obtained. The results showed that the chicken gut harbored more pathogens than the human gut. ESKAPE pathogens showed a stepwise increase from villagers to workers to chickens. The level of Streptococcus pneumoniae in workers was higher than that in villagers, indicating potential pathogen exposure risks. Chickens shared more ARGs with workers than villagers. Significantly higher abundances of 125 ARGs were detected in chicken samples compared to human samples. Among these, 22 ARGs were more abundant in worker samples than in villager samples. Metagenome-assembled genome (MAG) analysis revealed that 99 ARGs were annotated in human MAGs, predominantly in Escherichia coli (43 ARGs) and Klebsiella pneumoniae (22 ARGs). Co-occurrences of ARGs and mobile genetic elements (MGEs) were observed in E. coli and K. pneumoniae, with the transposon gene tnpA being carried by multiple bacteria. Co-localization of ARGs (APH(3’’)-Ib, APH(6)-Id) and MGE (IS91) in the MAG (Parasutterella gallistercoris) of workers was detected, while these two ARGs showed increasing abundance from villager to worker to chicken samples. This study indicated that chicken guts serve as important reservoirs of ARB and ARGs, which may influence the gut bacterial health of workers. Therefore, it is necessary to strengthen the management of antibiotic use in chicken farms and the health monitoring of relevant populations.
Extremely high mortality during early juvenile development remains the primary constraint to establishing sustainable aquaculture protocols for threatened seahorse species (Hippocampus spp.). Despite sustained efforts focused on nutritional optimisation, water quality control and pathogen suppression, survival rates have improved only marginally, suggesting that key underlying drivers remain insufficiently addressed. This conceptual review posits that juvenile mortality fundamentally constitutes a microbial ecological challenge, in which conventional rearing environments generate dysbiotic states that selectively favour opportunistic pathogens while failing to support protective microbial communities. Here we propose a microbiome-centric conceptual framework that reconceptualises the larval rearing unit as a dynamic microbial ecosystem, in which biofilm formation, microbial succession and host-microbe interactions collectively shape disease risk and larval survival. By integrating insight from biofilm ecology, probiotic research and biofloc technology, we synthesise dispersed findings to interpret larval mortality as an emergent outcome of disbiotic rearing environments, rather than isolated pathogenetic events. Emphasis is placed on ecological mechanisms, such as niche preemption, competitive exclusion and quorum quenching, rather than on taxonomic inventories of candidate probiotics. Finally, we translate this framework into a structured research agenda by identifying key knowledge gapes, testable hypothesis and operational implications for hatchery practices. By shifting the focus from pathogen eradication to microbial ecosystem engineering, this conceptual synthesis provides a foundation for more resilient and predictable seahorse aquaculture systems, offering a perspective applicable to other sensitive marine larval cultures.
Symbiotic microbial communities have been implicated in host resistance to pathogens, but their effects are rarely demonstrated experimentally in wildlife. This study tested how skin-associated bacterial communities (i.e., bacteriomes) influence infection by the chytrid fungus Batrachochytrium dendrobatidis (Bd) in two tropical frog species, Haddadus binotatus and Ischnocnema henselii, which differ in susceptibility to Bd. Using a 2x2 factorial experimental design, frogs of both species were assigned to treatments crossing Bd exposure and antibiotic-mediated bacteriome suppression. In parallel, we cultured 786 bacterial isolates from frog skin and assayed their ability to inhibit Bd in vitro, generating a functional database of Bd-inhibitory symbionts. Haddadus binotatus with an unsuppressed skin bacteriome and exposed to Bd showed no reduction in survival relative to Bd-unexposed controls, consistent with the lack of Bd infection previously observed in wild populations. In contrast, bacteriome suppression increased mortality and infection intensity under Bd exposure. Bd infection intensity in H. binotatus also decreased with the proportion of Bd-inhibitory sequence reads in the bacteriome, and a significant interaction between antibiotic treatment and Bd exposure affecting survival was detected, consistent with bacteriome-mediated protection in this species. In contrast, I. henselii experienced lower survival under Bd exposure in general. Species-specific log-rank tests revealed that bacteriome suppression significantly increased mortality under Bd exposure in H. binotatus but not in I. henselii, where survival was reduced under Bd exposure regardless of bacteriome state, suggesting fundamentally different defense strategies between species. Functional attributes of microbial communities, rather than diversity alone, appear to be key to disease outcomes. This work advances understanding of host–microbe–pathogen interactions and highlights microbiome function as a critical axis of wildlife disease defense.
Bacteriophages (phages) are pivotal regulators of microbiome ecology and function, yet their distribution, diversity and ecological roles within the bee gut remain largely unexplored, particularly across diverse bee species and geographic regions. Here, we used a large-scale metagenomic dataset to investigate phage communities associated with seven bee species across China. We recovered 121 viral operational taxonomic units (vOTUs) from 132 bee gut metagenomes, revealing that bee gut phages are dominated by the class Caudoviricetes and include numerous previously uncharacterized viral lineages. Biogeographic analyses revealed spatial structuring of phage communities such as latitudinal diversity gradient, distance–decay relationship. Variation partitioning analysis (VPA) indicated that bee host identity explained a substantially larger proportion of community variation than environmental factors. More, functional annotation further revealed that bee gut phages encode diverse carbohydrate-active enzymes (CAZymes) potentially involved in polysaccharide metabolism, as well as multiple anti-defense systems targeting bacterial antiviral mechanisms. Our study demonstrates that bee gut phages exhibit biogeographic structuring and host specificity. In addition, phages carry diverse functional genes that may influence bacterial metabolism and host–microbe interactions. These findings provide a comprehensive framework for understanding the ecological roles of phages in the bee gut and highlight their importance in shaping tripartite interactions among phages, bacteria, and bee hosts.
As a global cornerstone of animal protein, farmed shrimp production in China has been revolutionized by the Greenhouse Shrimp Farming Model (GSFM). However, the microbial mechanisms underpinning the productivity and biosafety of this intensive paradigm remain poorly understood. Through a large-scale metagenomic survey of 90 standardized aquaculture units in the core GSFM production regions of China, spanning a 15-degree latitudinal gradient, we deciphered the functional architecture of the GSFM microbiome. Our results reveal a striking functional convergence despite geographic taxonomic variation: while microbial compositions shifted across regions, the core metabolic pathways—particularly those governing nutrient cycling—remained conserved. High-productivity systems, notably in southern provinces (Guangxi and Guangdong), were characterized by a specialized microbial repertoire that optimized water chemistry through efficient nitrogen processing. We identified a sophisticated spatial division of labor, where the gut microbiota acts as a specialized nitrite detoxification unit, while the water column microbiota serves as the primary engine for ammonia assimilation. Furthermore, we characterized a diverse antibiotic resistome and utilized host-tracking to evaluate the ecological costs of intensification. These findings shift the focus from microbial identity to functional niche partitioning, providing a mechanistic blueprint for the sustainable intensification of aquaculture through targeted microbiome management. Characterized the microbial diversity within GSFM and highlighted the multifaceted contributions and potential value of these communities to the overall aquaculture system. Mapped the distribution of antibiotic-resistance genes in GSFM, identifying aminoglycoside, macrolide, and tetracycline resistance genes as the most prevalent, primarily associated with Proteobacteria, Bacteroidetes, and Actinobacteria. Annotated nitrogen-cycle genes, showing that gut microbiota are enriched in nitrite-metabolizing genes, while water microbiota possess great ammonium-metabolizing capacity, highlighting a complementary metabolic division of labor that underpins GSFM’s adaptation to high nitrogen loads. The division of labour between aquatic and intestinal microbiota in nitrogen metabolism may be the key to promoting high GSFM production.
This study primarily investigated the differences in rumen microbial composition and functional profiles among goats with varying degrees of rumen bloat under a high-concentrate diets (HCDs) feeding condition. Forty Nubian goats fed a HCDs were selected as experimental animals and subjected to rumen bloating (RB) scoring. From these, six goats with high bloat scores (HB group) and six goats without obvious bloat (NB group) were selected. Rumen content samples were collected via oral stomach tubes. Rumen fluid foaming characteristics and pH values were measured, and metatranscriptome sequencing was conducted to analyze microbial functions. The results demonstrated that compared to the NB group, the HB group exhibited significantly higher foaming capacity, foam stability, and viscosity of ruminal fluid, along with a significantly lower pH value (P < 0.05). Additionally, α-diversity indices (Chao1, ACE, and observed_species) were significantly elevated in the HB group (P < 0.05). Annotation of rumen microbial species showed that the relative abundance of Ascomycota, Basidiomycota, Dialister, and Dialister sp. CAG:486 was significantly higher in the HB group, whereas Bacteroidetes, Proteobacteria, Spirochaetes, Prevotella, Bacteroides, Treponema, Lactobacillus, Leptotrichia hofstadii and Prevotella oralis were significantly reduced (P < 0.05). Functional analysis of differentially expressed genes (DEGs) revealed significant enrichment in several biological processes. In the Gene Ontology (GO) database, DEGs were predominantly associated with cellular protein modification, protein maturation, and ribosome biogenesis. According to KEGG pathway analysis, DEGs were mainly enriched in pathways related to endocytosis, ubiquitin-mediated proteolysis, and protein processing in the endoplasmic reticulum. In summary, under uniform feeding conditions, individual variations in goat rumen microbiota functions are associated with differences in microbial community structure and gene expression patterns. Alterations in the protein metabolism function of the rumen microbiome are associated with the presence of foaming proteins, which in turn are linked to individual differences in rumen foam production capacity. Ultimately, these associations may result in differing susceptibility and severity of RB among animals.
Heat stress (HS) is a pervasive environmental hazard in intensive poultry production that severely impairs skeletal health and causes substantial economic losses. While emerging evidence links gut microbiota dysbiosis to bone metabolism, its causal role in mediating HS-induced bone loss remains poorly defined. Here, we established a chicken model of HS and employed fecal microbiota transplantation (FMT) to investigate the mechanistic link between gut microbiota and skeletal deterioration. Our results demonstrated that HS reduced growth performance, disrupted gut microbial community structure, and impaired bone microarchitecture and biomechanical strength. Critically, FMT from HS-exposed donors recapitulated the key features of HS-induced bone loss in recipient chickens, characterized by impaired trabecular bone microarchitecture, reduced biomechanical strength, and enhanced bone resorption-related gene expression. Mechanistically, the HS-microbiota induces functional dysbiosis, characterized by a relative increase in the abundance of the genus Turicibacter, while compromising intestinal barrier integrity, triggering an inflammatory response, and inhibiting intestinal mineral absorption. Collectively, these factors contribute to reduced bone performance. These findings establish the gut microbiota as a key mediator of HS-induced bone loss, providing a novel mechanistic framework for understanding host–microbiota–environment interactions in the context of environmental hazards, which has broader implications for animal health and environmental toxicology.
Post-weaning estrus return is critical for sow reproductive efficiency. The gut microbiota is associated with post-weaning estrus of sows, potentially through effects on nutrient utilization and metabolic regulation. However, current microbial signatures associated with estrus return remain poorly resolved at the strain-level. Here, we explored the relationship between the gut microbiome and post-weaning estrus in sows using metagenomics and metabolomics profiling of 85 fecal samples. From 2,704 non-redundant metagenome-assembled genomes (MAGs), 608 estrus-associated MAGs were identified by LEfSe analysis. Among these, 48 high-quality MAGs were selected for co-abundance network analysis, which revealed two competing microbial functional guilds. Guild 1 was significantly enriched in the normal group, harboring more β-glucosidase and folate biosynthesis genes, but fewer antibiotic resistance genes and virulence factors than Guild 2. A random forest model based on these 48 MAGs demonstrated excellent performance in distinguishing between the normal and non-return sows (AUROC = 0.946) and was validated in an independent dataset (n = 29, AUROC = 0.818). Additionally, the guild-level microbiome index (GMI) derived from abundance differences between the two guilds also showed good discriminatory power (AUROC = 0.799). Integrated multi-omics analysis revealed alterations in fecal bile acid metabolism in non-return sows, characterized by a significantly increased ratio of secondary to primary bile acids and the accumulation of specific secondary bile acids. Notably, the enrichment of the Clostridia strain SFHK01 sp016296675, a member of Guild 2, and its encoded 12α-HSDH gene was positively associated with specific secondary bile acids, suggesting that this specific strain is involved in the distinct metabolic alterations observed in non-return sows. These findings provide the genome-resolved and guild-based insights into the gut microbial signatures associated with post-weaning estrus return, offering a basis for potential microbiota-targeted interventions to improve sow reproductive performance.
The gastrointestinal microbiota is a key determinant of vertebrate physiology, metabolism, and adaptation, forming a dynamic holobiont system that supports host health and resilience. However, while the gut microbiota of several fur seal species has been described, most studies have focused primarily on taxonomic composition, leaving a major gap in understanding how microbial communities influence host physiology in marine mammals. This study provides the first comprehensive comparison of the faecal microbiota and blood metabolomic profiles of Australian (Arctocephalus pusillus doriferus) and New Zealand fur seals (A. forsteri) across age classes (adult vs. pup), integrating 16S rRNA gene sequencing, and untargeted metabolomics and untargeted lipidomics to examine host–microbe interactions. Adult fur seals exhibited a conserved microbial structure dominated by the phyla Bacillota, Fusobacteriota, and Bacteroidota, while pups displayed lower microbial diversity and higher relative abundances of Actinobacteriota and Campylobacterota, alongside enrichment of metabolites involved in DNA synthesis (2-deoxy-D-ribose, 2-deoxycytidine, and 2-deoxyuridine) and lipid metabolism. Correlations between bacterial taxa and metabolites implicated in growth, fat deposition, and hair development suggest that it is possible that early-life microbial communities may play an important role in supporting rapid development and thermoregulation. Despite logistical constraints inherent to field-based sampling of wild marine mammals, our findings demonstrate consistent microbial patterns within the Arctocephalus genus and clear age-related differences in blood metabolic profiles. Together, these results enhance understanding of the complex interplay between host development, diet, and microbial ecology in fur seals, and establish a foundation for future research into the functional significance of microbiota in marine mammal health and adaptation. Not applicable.
The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience. We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps. Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.
Livestock grazing on saline-alkali pastures frequently encounter nutritional challenges due to inadequate forage quality and imbalanced rumen function. Phytogenic feed additives, which are abundant in bioactive compounds such as tropane alkaloids and flavonoids, have demonstrated potential in enhancing rumen fermentation and improving animal performance. Przewalskia tangutica, a desert plant rich in these compounds, remains largely unexplored concerning its effects on microbiota and metabolism in sheep under saline-alkali conditions. This study aims to evaluate the impact of graded supplementation of Przewalskia tangutica on rumen fermentation, microbial dynamics, digestive enzyme activity, and growth performance in sheep grazing on degraded saline-alkali pastures. Supplementation with Przewalskia tangutica significantly increased the average daily gain (ADG, P < 0.001) and reduced the feed conversion ratio (FCR, P < 0.001). The high-dose group (HP) exhibited the highest ADG at 139.94 g/d. Additionally, the concentrations of total volatile fatty acids (VFAs), including acetate, isobutyrate, and butyrate, were significantly elevated (P < 0.001), peaking at 1.46 mmol/L in the HP group. Furthermore, the activities of amylases, lipase, cellulase, and protease increased significantly (P < 0.05). While the bacterial alpha diversity remained unchanged, beta diversity analysis revealed structural shifts characterized by increased abundances of Verrucomicrobiota, Proteobacteria, and Fibrobacterota (P < 0.05). Fungal diversity also increased under the HP treatment (P < 0.05), whereas a reduction in Cladosporium abundance was correlated with enhanced fiber degradation. Moreover, microbial co-occurrence networks demonstrated more balanced interactions in the treated groups, with significant correlations among taxa, enzymes, and VFAs. Przewalskia tangutica improves rumen fermentation and sheep performance in saline-alkali environments through targeted modulation of microbial communities and enzymatic activity, particularly at the high dose, significantly improved sheep growth performance by increasing average daily gain and reducing the feed conversion ratio, suggesting a sustainable strategy for livestock production in challenging ecosystems. This study highlights Przewalskia tangutica as a breakthrough phytogenic solution for livestock production in saline-alkali regions, where poor forage quality and microbial dysbiosis limit productivity. Supplementation significantly enhanced sheep growth (↑ADG, ↓FCR) and rumen fermentation (↑VFAs) by modulating microbial communities—enriching fiber-degrading Fibrobacterota while suppressing salinity-tolerant Cladosporium fungi. These shifts correlated with improved fiber utilization and enzyme activities, directly addressing rumen inefficiencies under saline stress. By leveraging native plant bioactives, this strategy revitalizes degraded pastures, reduces dependency on synthetic additives, and enhances climate resilience in arid ecosystems. These findings provide a sustainable blueprint for optimizing livestock performance in marginal environments and advancing food security and ecological restoration in salt-affected regions globally.
