Animal Microbiome

In aquaculture, the secretions of cultured organisms contribute to the development of aquatic antibiotic resistance. However, the antibiotic-induced changes in fish feces remain poorly understood. This study aimed to assess the short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) upon antibiotic treatment and withdrawal period.

Min Kyo Kim

Yoonhang Lee

Jiyeon Park

Ju-Yeop Lee

Hyo-Young Kang

Young-Ung Heo

Do-Hyung Kim

Anim Microbiome

Short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) following antibiotic treatment and withdrawal

抗生素处理及停药后虹鳟幼鱼（Oncorhynchus mykiss）粪便微生物组和抗生素耐药性的短期动态变化

Abstract Background Enterotoxigenic Escherichia coli ( E. coli ) is one of the most prevalent causes of diarrhea in young animals. Postbiotics derived from yeast have the potential to positively influence the mucosal microbiota in the jejunum, therefore it was hypothesized that Saccharomyces yeast postbiotics could enhance the microbiota and mucosal immune response in the jejunum, mitigating the effects of infection with enterotoxigenic E. coli . The purpose of this study was to investigate the effects of a Saccharomyces yeast postbiotic on the mucosal microbiota and mucosal immune response in the jejunum of newly weaned pigs challenged with F18 + E. coli. Results Thirty-six individually housed nursery pigs were allotted into three treatments utilizing a randomized complete block design; negative control (NC: basal diet, no challenge), positive control (PC: basal diet, challenge), and SYP (basal diet + Saccharomyces yeast postbiotics at 175 g/ton , challenge). On d 7, PC and SYP were orally inoculated with F18 + E. coli , whereas NC received saline. On d 28, pigs were euthanized for sampling of the jejunum to analyze the mucosal microbiota, oxidative stress, immune status, and intestinal morphology. The PC reduced ( P &lt; 0.05) growth performance compared to NC. The SYP improved ( P &lt; 0.05) fecal score from d 7–18 when compared with PC. SYP reduced ( P &lt; 0.05) protein carbonyl, reduced ( P &lt; 0.05) gene expression of Toll-like receptor 4, and increased ( P &lt; 0.05) gene expression of mammalian target of rapamycin, compared with PC. Conclusions Challenge with F18 + E. coli negatively impacted jejunal mucosa-associated microbiota and jejunal morphology, affecting growth performance. Saccharomyces yeast postbiotics could reduce the negative effects associated with F18 + E. coli infection.

Alexa R. Gormley

Marcos Elias Duarte

Zixiao Deng

Sung Woo Kim

Saccharomyces yeast postbiotics mitigate mucosal damages from F18+ Escherichia coli challenges by positively balancing the mucosal microbiota in the jejunum of young pigs

酿酒酵母后生元通过正向平衡幼猪空肠黏膜微生物群缓解F18+大肠杆菌攻击引起的黏膜损伤

Abstract Heterogeneity of the rearing environment in farmed animals can improve welfare and stocking success by enhancing natural behaviours, reducing stress, and decreasing pathogen occurrence. Although microbial diversity is often associated with well-being, their direct and indirect effects on health of farmed animals remain underexplored. We examined the impact of structural heterogeneity of aquaculture tanks on microbial communities in tank biofilm and fish gut microbiome. Enrichment (stones and shelters) significantly promoted microbial diversity and community homogeneity in tank biofilm. However, diversity of gut microbiome did not depend on rearing treatment or microbial composition of the environment. Fish in enriched tanks exhibited greater compositional variation in gut microbiome than those in standard tanks. Tanks without enrichments had higher occurrence of potentially pathogenic bacterial families ( Corynebacteriaceae and Staphylococcaceae ), while enriched tanks had more beneficial gut microbes ( Lactobacillus ). Microbial diversity in tank biofilm was negatively associated with fish mortality during a natural epidemic of Flavobacterium columnare , suggesting a protective effect of diverse microbial communities. These findings support environmental enrichment in mitigating disease outbreaks through enhanced microbial diversity, providing important implications for disease control and sustainable health management in aquaculture.

Roghaieh Ashrafi

Lotta-Riina Sundberg

Pekka Hyvärinen

Anssi Karvonen

Heterogeneity of the rearing environment enhances diversity of microbial communities in intensive farming

饲养环境的异质性增强集约化养殖中微生物群落的多样性

The composition and function of animal gut microbiota are shaped by various factors, among which diet is one of the major factors. Diet is affected by seasonal shifts and geographical differences, which in turn impact the host's nutritional levels. To adapt to these environmental changes, the gut microbiome often produces matching responses. Understanding the relationships among the environment, diet, host and the gut microbiome is helpful for exploring the environmental adaptation of wildlife. Here, we chose wild sika deer (Cervus nippon), which is composed natural allopatric populations, to explore how the environment shapes the gut microbiome and affects the relationship between microbiota composition and function and the mutual adaptation of the seasonal living environment to seasonal dietary changes. To this purpose we used DNA metabarcoding, 16S RNA gene amplification sequencing, metagenomic shotgun sequencing and nutritional analyses to comprehensively examine the relationships among the forage plant, nutrient status and host gut microbiome. Our analyses showed spatiotemporal differences in diet between the Tiebu and Hunchun regions, which ultimately led to varying intakes of protein, cellulose, and soluble sugar. The microbiome composition and function showed unique characteristics in each group, and significant differences were detected at the gene level for the protein absorption and metabolism pathway, the carbohydrate metabolic absorption pathway, and cellulase enzyme function, which are related to nutrition. We also found differences in the pathogenic bacteria and resistance mechanisms genes of the gut microbiota in different groups. Our results showed that the gut microbiome of allopatric populations adapts to changes in food composition and nutrition in different seasons and areas to help the host cope with spatiotemporal changes in the living environment. At the same time, varying levels of human activity can have potential health impacts on wild animals.

Xiaofan Ma

Xiaoyu Hu

Kai Liu

Wei Wang

Wei Jia

Huayao Gao

Ming Lu

Jie Liu

Yunfeng Chen

Yingjie Ma

Yumei Li

Yonggang Nie

Spatiotemporal differences induced changes in the structure and function of the gut microbiota in an endangered ungulate

时空差异诱导濒危有蹄类动物肠道微生物群结构和功能的变化

Antibiotic use has undesirable side-effects on the host, including perturbations of gut microbiota, immunity, and health. Mammalian studies have demonstrated that concomitant/post antibiotic use of pro-, pre-, and synbiotics could re-establish gut microbiota and prevent detrimental host effects. However, studies evaluating similar effects in fish are scanty. This study evaluated the effects of dietary supplementation with a synbiotic mixture on the post-smolt Atlantic salmon gut microbiota, growth performance, and health during antibiotic treatment and subsequent recovery. Fish in five tanks each were fed either a commercial control diet or a synbiotic diet containing Pediococcus acidilactici and fructo-oligosaccharides, for 6 weeks (S1). Then, fish in three tanks per treatment were fed with medicated diets, containing 3500 ppm florfenicol coated onto the control or synbiotic diets, for 2 weeks (S2) and refed with the respective nonmedicated diets for another 3 (S3) and 5 (S4) weeks of recovery period. The fish not subjected to medication were fed the control or synbiotic diets throughout the experimental period. Samples were collected at S1-S4 from both the nonmedicated and medicated fish. Florfenicol decreased the feed intake in control group. It reduced the growth rate in both control and synbiotic groups with lesser reduction in synbiotic group. Florfenicol did not significantly affect observed taxa and Shannon indexes. Bacterial composition before and after medication clustered distinctly in control and clustered together in synbiotic groups. Lactobacillus dominated in control while Lactobacillus and Pediococcus dominated in synbiotic group during medication and recovery. Florfenicol did not significantly influence the immune or stress response marker gene expressions, though the expression patterns differed between diet groups. Florfenicol did not cause inflammation in the distal intestine or change hepatosomatic index. This study highlighted the negative impact of a two-week florfenicol treatment on feed intake and growth performance in Atlantic salmon, with moderate effects on gut microbiota and gene expression. Concomitant use of a synbiotic diet helped to maintain the gut microbial composition and influenced the performance positively and immune gene expressions differently during medication. This study indicates the importance of nutritional interventions through synbiotic supplementation as a possible strategy for managing Atlantic salmon during antibiotic treatment.

Anusha K. S. Dhanasiri

Yanxian Li

Åshild Krogdahl

Torunn Forberg

Trond M. Kortner

Longitudinal study on the effects of a synbiotic supplement to Atlantic salmon diets on performance, gut microbiota and immune responses during antibiotic treatment and subsequent recovery

关于合生元补充剂对大西洋鲑鱼在抗生素治疗期间及后续恢复过程中生长性能、肠道微生物群和免疫反应影响的纵向研究

Abstract Background Species host diverse microbial communities that can impact their digestion and health, which has led to much interest in understanding the factors that influence their microbiota. We studied the developmental, environmental, and social factors that influence the microbiota of nestling barn owls ( Tyto alba ) through a partial cross-fostering experiment that manipulated the social and nest environment of the nestlings. We then examined the nestling microbiota before and three weeks after the exchange of nestlings between nests, along with the microbiota of the adults at the nest and nestlings in unmanipulated nests. Results We found that nestlings had higher bacterial diversity and different bacterial communities than adults. The microbiota of nestlings was more like that of their mothers than their fathers, but the similarity to the father tended to increase with the amount of time the father was in close proximity to the nest, as measured from movement data. Cross-fostered offspring had higher bacterial diversity and greater changes in bacterial community composition over time than control offspring. Cross-fostering led the microbiota of the nestlings in the experiment to converge on similar bacterial communities. The microbiota of nestling owls therefore rapidly changed along with alterations to their social and nest environments. Conclusions These results highlight the dynamic nature of the microbiota during early development and that social interactions can shape microbial communities.

Ammon Corl

Motti Charter

Gabe Rozman

Sondra Turjeman

Sivan Toledo

Pauline L. Kamath

Wayne M. Getz

Ran Nathan

Rauri C. K. Bowie

Social, environmental, and developmental factors affect the microbiota of barn owls (Tyto alba) in a cross-fostering experiment

在交叉寄养实验中，社会、环境和发育因素影响仓鸮（Tyto alba）的微生物群

Dogs—whether pets, rural, or stray—exhibit distinct living styles that influence their fecal microbiota and resistomes, yet these dynamics remain underexplored. This study aimed to analyze and compare the fecal microbiota and resistomes of three groups of dogs (37 pets, 20 rural, and 25 stray dogs) in Shanghai, China. Metagenomic analysis revealed substantial differences in fecal microbial composition and metabolic activities among the dog groups. Pet dogs displayed the lowest microbial diversity. Using Shapley Additive Explanations (SHAP), an interpretable machine learning approach, Ligilactobacillus emerged as the most diverse genus, with significantly higher SHAP values in stray dogs, suggesting enhanced adaptability to more variable and less controlled environments. Across all samples, 587 antibiotic resistance genes (ARGs) were identified, conferring resistance to 14 antibiotic classes. A striking observation was the detection of mcr-1 in one pet dog, indicating a potential public health risk. The floR gene was identified as a key differentiator in resistance profiles, particularly in pet and rural dogs, likely due to antibiotic exposure in their environments. This study provides the first comprehensive assessment of fecal microbiota and resistome variations among dogs with different lifestyles, revealing a less resilient microbiome and heightened antimicrobial resistance in pet dogs, which could have public health implications.

Nan Zhou

Weiye Chen

Luming Xia

Min Li

Huiping Ye

Chao Lv

Yiwen Chen

Zile Cheng

Tae-Jin Park

Pak-Leung Ho

Xin Gao

Xiaokui Guo

Hongjin Zhao

Huiluo Cao

Yongzhang Zhu

Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles

宏基因组学揭示不同生活方式犬类的抗性组、移动组和毒力组

Abbreviation	anim microbiome
Journal Impact	4.74
Quartiles(Global)	VETERINARY SCIENCES(Q1)

ISSN	2524-4671
h-index	22

Publication Information	Publisher: BioMed Central Ltd，Publishing cycle: ，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 2019，Proportion of original research papers: 94.20%，Self Citation Rate:6.10%， Gold OA Rate: 100.00%
Journal Fees	$2090Details
Average review cycle	网友分享经验：13 Weeks

Animal Microbiome

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Short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) following antibiotic treatment and withdrawal

Saccharomyces yeast postbiotics mitigate mucosal damages from F18+ Escherichia coli challenges by positively balancing the mucosal microbiota in the jejunum of young pigs

Heterogeneity of the rearing environment enhances diversity of microbial communities in intensive farming

Spatiotemporal differences induced changes in the structure and function of the gut microbiota in an endangered ungulate

Longitudinal study on the effects of a synbiotic supplement to Atlantic salmon diets on performance, gut microbiota and immune responses during antibiotic treatment and subsequent recovery

Social, environmental, and developmental factors affect the microbiota of barn owls (Tyto alba) in a cross-fostering experiment

Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles

Short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) following antibiotic treatment and withdrawal

Saccharomyces yeast postbiotics mitigate mucosal damages from F18+ Escherichia coli challenges by positively balancing the mucosal microbiota in the jejunum of young pigs

Heterogeneity of the rearing environment enhances diversity of microbial communities in intensive farming