Aedes aegypti mosquitoes are the main vector of pathogens like dengue virus and chikungunya virus. The immature life stages of mosquitoes share the same habitat with a variety of microorganisms in aquatic environments. To better understand the microbial diversity in field-derived Ae. aegypti, we analysed simultaneously collected larvae, pupae, and freshly emerged adults from Burkina Faso together with their breeding water via 16S rRNA gene sequencing. We observed a decrease in bacterial diversity and load across the mosquito life stages. At the phylum level, a strong increase in relative abundance of Proteobacteria was found along the mosquito stages. The same 40 amplicon sequence variants were consistently found as most abundant in the adults, regardless of the sample collection site, and all belonged to the Gammaproteobacteria. Our data suggest that these bacteria were not randomly derived by chance from the environment in the mosquito but rather deposited by a female mosquito during oviposition, a transmission route recently coined as "diagonal transmission". Indeed, our results indicated that there is a selection of Gammaproteobacteria from the breeding water and that these bacterial members are further maintained from larvae to adults. This study provided new data on the microbiome composition of field-collected Ae. aegypti, contributing to an enhanced understanding of the origin and colonization route of the mosquito microbiome, potentially via a diagonal transmission route.

Dietary trace mineral (TM) concentrations for lactating cows often exceed national recommendations under commercial feeding practices. Excess TM supplementation may exert selection pressure on the gut microbiota, promoting metal resistance and potentially co-selecting for important antimicrobial resistance genes (ARGs). This study used a cross-over design to investigate the impact of overfeeding a commericially representative TM premix on the gut microbiome and resistome of lactating dairy cattle. Cows were fed either recommended or surplus TM levels for 31 days followed by sample collection from rumen papillae, whole rumen content, and feces. Targeted amplicon, shotgun metagenomic sequencing, and droplet digital PCR (ddPCR) were used to assess microbial community compositions and the associated resistome. While a surplus TM did not significantly affect the overall microbial diversity, specific taxa differed between the matrices and to a lesser extent by diet. Spirochaetota were more abundant in papillae of cows fed the recommended TM diet, whereas Bacillota were more prevalent in the rumen and feces from cows fed the surplus TM. Phosphorus had the greatest impact on prokaryotic taxa in rumen content. Cows fed surplus levels of TM showed increased abundances of Ruminococcus in their rumen, but decreased Campylobacter, Desulfovibrio, and Treponema adhered to their rumen papillae, Methanosphaera in their rumen and feces, as well as Treponema in their feces. Despite these changes, no significant differences in the presence of key ARGs or metal resistance genes were detected by metagenomics, and ddPCR showed no significant impact of TM supplementation on blaCTX−M, pcoA and zntA gene levels. Overfeeding TM in a commercial premix resulted in modest matrix specific shifts I the microbial composition without detectable enrichment of selected ARGs or metal resistance genes. These findings suggest short-term resilience of the rumen ecosystem to surplus TM supplementation. Additionally this work provides foundational knowledge to further guide mechanistic and long-term investigations.

Hibernation enables animals to survive extreme environments, yet gut microbiome dynamics across the full hibernation cycle remain poorly understood, particularly in chiropterans with unique physiological traits. This study aimed to precisely characterize seasonal microbial succession in wild Rhinolophus sinicus using 16S rRNA gene sequencing across 6 physiological stages, with a focus on taxonomic and functional shifts linked to hibernation-associated fasting and post-hibernation activity. Alpha diversity followed a pronounced V-shaped trajectory, declining during hibernation and recovering only gradually—remaining suppressed in the early active stage and rebounding markedly by mid–late active stages. Beta diversity revealed a clear separation between hibernation and active phases, with physiological stage explaining 34.9% of community variation. At the phylum level, Pseudomonadota was the dominant taxon during hibernation, while Bacillota became the most abundant phylum in the active period. At the genus level, Yokenella was the core genus in the hibernation stage, and Lactococcus was the dominant genus in the active period. Functional predictions showed enrichment of lipid and amino acid metabolism during hibernation, supporting energy maintenance under fasting, while active-phase microbiota were oriented toward carbohydrate metabolism, matching increased energy demands. Our findings demonstrate that hibernation drives directional restructuring of the gut microbiota in R. sinicus, offering new insights into microecological strategies underlying bat survival under extreme conditions.

Gut microbial dysbiosis is a common cause of calf diarrhea, a major contributor to calf mortality. Additionally, the early gut microbiota in calves is considered a hotspot for antimicrobial resistance, potentially leading to the failure of antibiotic treatments. Most prior research investigating the associations between calf microbiota and diarrhea has relied on partial 16S rRNA gene amplicon sequencing, which offers limited taxonomic resolution. In this study, we collected fecal samples from 25 Holstein-Angus crossbred neonatal calves on days 4, 7, 11, 14, and 30 and analyzed the gut microbiota using full-length 16S rRNA gene amplicon sequencing. A machine-learning approach was employed to identify potential bacterial markers associated with diarrhea. A significant increase in gut microbial diversity (P < 0.05) was observed with the calves’ age; however, days 11 and 14 showed similar diversity levels, coinciding with the peak prevalence of diarrhea. Differences in gut microbiota features between healthy (n = 5) and diarrheic calves (n = 8), determined by fecal scores on days 11 and 14, were also detected at earlier (day 4) and later (day 30) stages of life. Seven diarrhea-associated species (e.g., Fusobacterium spp. and Bacteroides fragilis) and four health-associated species (e.g., Megasphaera elsdenii and Enterococcus faecium) were consistently identified by both Linear Discriminant Analysis Effect Size (LEfSe) analysis and Boruta feature selection. Machine learning models trained on Boruta-selected bacterial features using Random Forest and Support Vector Machine algorithms achieved high classification accuracy (87–100%) in distinguishing diarrheic from healthy fecal samples. Moreover, the concentration of gut bacteria resistant to the cephalosporin antibiotic cefotaxime was significantly higher in diarrheic calves that harbored a greater abundance of pathogens (P < 0.05), particularly on days 11 and 14, when the prevalence of diarrhea was high, which may be attributed to the co-localization of virulence genes and antimicrobial resistance genes. This study provided a comprehensive characterization of the neonatal calf gut microbiota, identified potential bacterial species as biomarkers to predict diarrhea and probiotic candidates, and indicated early, immediate, and long-term microbiota changes associated with diarrhea. Additionally, it highlighted the increased risk of antimicrobial resistance to antibiotic treatment in diarrheic calves.

BackgroundThe nutritional status of ewes during gestation and lactation is a key determinant of lamb growth performance. Supplementation with rumen-protected L-arginine (RP-Arg) during these stages induces maternal metabolic adaptation, thereby maintaining fetal developmental homeostasis. However, the sustained effects of such metabolic regulation on postnatal lamb growth and immune functions are currently unclear. Twenty-seven pregnant Chinese Merino ewes (at 60 days of gestation) were randomly assigned to one of three dietary treatments: (1) grazing only (control, CON), (2) grazing plus 300 g/day of concentrate feed (SF), or (3) SF diet supplemented with 30 g/day of RP-Arg (ARG). When the lambs reached 14 days of age, ileal and liver tissues were collected. The ileal microbiota was characterized using 16S rRNA gene amplicon sequencing, and untargeted metabolomics was used to examine the hepatic metabolism in the lambs.ResultsCompared with the CON group, both SF and ARG group lambs showed significantly improved early growth performance (P < 0.05), and the ARG group exhibited significantly higher average daily gain and total weight gain (net weight gain) than the SF group (P < 0.05). Milk protein content was significantly higher in the SF and ARG groups than in the CON group (P < 0.05). Notably, compared with the SF group, ARG supplementation elevated colostrum lactoferrin and insulin-like growth factor-1 (IGF-1) concentrations by 28.4% and 34.1%, respectively (P < 0.05). Compared with SF group, ARG group showed a higher relative abundance of ileal Bacteroidota (+ 40%, P < 0.05) and Prevotella (+ 96%, least discriminant analysis > 3.2), increased hepatic glutamine, methionine, and malate (variable importance in projection > 1.3, P < 0.05), and upregulated arginine-proline metabolism and ABC transporters, indicating that RP-Arg was associated with a shift in both the ileal microbiota and hepatic metabolite profile, suggestive of a modest gut-liver metabolic interaction to enhance nitrogen and energy flux, resulting in superior lamb growth.ConclusionsRP-Arg specifically elevates colostrum IGF-1 and lactoferrin levels, enriches ileal Bacteroidota and Prevotella, and reprograms hepatic arginine-proline and ABC transporter metabolism. Overall, these changes were associated with an increased early growth rate of lambs without affecting milk protein production.Graphical Supplementary InformationThe online version contains supplementary material available at 10.1186/s42523-026-00526-z.

The rumen microbiota plays a pivotal role in the growth performance of host animals, primarily due to its ability to ferment ingested feed. Hulunbuir sheep exhibited a slow growth rate compared to other local breeds. A deeper comprehension of the development of the rumen bacteria community in Hulunbuir sheep can offer insights into the factors contributing to their slow growth rate. This study utilized metagenomic analysis of rumen content samples from Hulunbuir sheep to investigate the patterns of microbial growth and their relationship with the ADG. The results of the PCoA and enterotype analyses demonstrated that the ruminal bacterial community developed distinct characteristics following weaning. The dominant bacterial phyla in the rumen of Hulunbuir sheep, Bacteroidetes and Firmicutes, exhibited a significant age-related change. At the genus level, while the abundance of dominant bacterial genera changed with the growth of Hulunbuir sheep, Prevotella consistently maintained a high abundance across all age time points. We then examined the effects of age on microbial function by analyzing carbohydrate-metabolizing enzymes and protein-metabolizing peptidases. The abundance of carbohydrate-metabolizing enzymes decreased with growth, while peptidases showed opposite dynamics. Under the current feeding conditions correlation analysis showed that the abundances of Firm-04, CAG-83, and GCA-900,199,385 were negatively correlated with ADG (R<-0.4, p < 0.05), while the abundance of Ga6A1 was positively correlated with ADG (R > 0.5, p < 0.05). In addition, we found 67 MAGs related to ADG, which are capable of secreting carbohydrates-metabolizing enzymes and peptidase. This study uncovers the temporal dynamics of rumen microbiota development during the early to late fattening phase and identifies microbes associated with ADG, which could inform strategies to improve growth and production efficiency.

Astroviruses (AstVs) are single-stranded RNA viruses belonging to the family Astroviridae, which comprises two genera: Mamastrovirus (MaAstV) and Avastrovirus. These viruses circulate globally and infect multiple hosts, enabling cross-species transmission that poses significant risks to both humans and animals. In this study, we comprehensively analyze the evolution, global geographic transmission, and cross-species transmission of MaAstVs. Our analysis reveals that a broad distribution and diverse host range for AstVs, with a noticeable decline in detection after 2017. Phylogenetic analyses uncover complex relationships, suggesting potential host spillover events. The evolutionary rates of different MaAstVs vary. Most MaAstVs exhibited a decreasing trend in effective population size, with minor fluctuations observed in a few instances. Furthermore, our global transmission analysis demonstrates the spread of MaAstVs across Asia, Europe, the Americas, Africa, and Oceania, identifying specific countries as key nodes within the transmission network. Analyses of cross-species transmission in Groups 1, 2, and 3 reveal distinct ancestral origins and trace the cross-species transmission history of MaAstVs among domestic animals, humans, companion animals, and wildlife. This study offers a detailed examination of the evolution, global transmission, and cross-species transmission of MaAstVs across multiple hosts. Our findings provide valuable insights into their circulation across species and regions, as well as their evolutionary dynamics.