Animal microbiome最新文献

{"title":"Increasing the level of hemicelluloses in the lactation diet affects the faecal microbiota of sows and their piglets without affecting their performances.","authors":"Francesco Palumbo, Paolo Trevisi, Federico Correa, Giuseppe Bee, Marion Girard","doi":"10.1186/s42523-024-00354-z","DOIUrl":"10.1186/s42523-024-00354-z","url":null,"abstract":"<p><strong>Background: </strong>Specific sources of dietary fibres in sow gestation and lactation diets, such as inulin or wheat bran, have been shown to affect both the sow and its litter health by modulating the piglet's intestinal microbial population and composition. However, only a few studies have reported the effects of some specific fractions of the cell wall of the plants in the sow's lactation diet. Therefore, this study investigates the effect of increasing the level of HCs in a sow's lactation diet on the nutrient apparent total tract digestibility (ATTD), the faecal volatile fatty acid (VFA) profile, the microbiota of the sow and the microbiota and the performances of slow-growing (SG) and fast-growing (FG) piglets.</p><p><strong>Results: </strong>Increasing HCs level increased (P < 0.05) the proportions of butyrate and valerate on day 3, and the ATTD of acid detergent fibres (ADF), neutral detergent fibres (NDF), and gross energy and decreased (P < 0.05) the proportion of propionate on day 17, and the ATTD of crude protein. The beta diversity was affected (r² = 0.11; P = 0.02) by the maternal dietary treatments with 11 common genera differing (P < 0.05) in the sow's faecal microbiota, and five in the piglet's microbiota. Regardless of the maternal dietary treatment, SG piglets had a lower (P < 0.05) proportion of isobutyrate and isovalerate, a lower (P < 0.05) abundance of Lachnospiraceae_XPB1014_group, Enterococcus, and Succinovibrio genera, and a greater (P < 0.05) abundance of Olsenella than FG piglets.</p><p><strong>Conclusions: </strong>Increased HCs level in a sow's lactation diet affects the ATTD of nutrients, the faecal VFA and microbiota profiles of the sows with limited effects on SG and FG piglets' faecal microbiota and no effects on the performance or VFA profile of these piglets.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"68"},"PeriodicalIF":4.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-strain probiotics enhance growth, anti-pathogen immunity, and resistance to Nocardia seriolae in grey mullet (Mugil cephalus) via gut microbiota modulation.","authors":"Ching-Hung Chan, Li-Han Chen, Kuang-Yu Chen, I-Hung Chen, Kung-Ta Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Eric Y Chuang, Ming-Tse Lin, Tsong-Rong Yan","doi":"10.1186/s42523-024-00353-0","DOIUrl":"https://doi.org/10.1186/s42523-024-00353-0","url":null,"abstract":"<p><p>Grey mullet (Mugil cephalus) aquaculture is economically vital due to the high value of its roe. However, it faces significant risks from disease outbreaks, particularly from Nocardia seriolae. Current reliance on antibiotics has drawbacks, highlighting the potential of probiotics as a promising alternative. Despite this, no studies have focused on the effects and mechanisms of probiotics in disease prevention and treatment in grey mullet. This study, therefore, investigates the efficacy of probiotics in enhancing disease resistance and promoting growth in grey mullet. Three strains of probiotics, Lacticaseibacillus rhamnosus FS3051, Limosilactobacillus reuteri FS3052, and Bacillus subtilis natto NTU-18, were selected to evaluate their anti-N. seriolae activity and hydrolytic enzyme secretion in vitro. Then, 144 grey mullet were randomly divided into four groups: control, L. rhamnosus FS3051, L. reuteri FS3052, and B. subtilis natto NTU-18. After being fed the corresponding diet for 28 days, fish were measured for immune gene expression and short-term growth followed by challenge of N. seriolae. Survival rates were recorded for 35 days post challenge. Additionally, the gut microbiota of the control and probiotic groups with effects on both growth and protection against N. seriolae were analyzed to investigate the potential role of gut microbiota. Results demonstrated that L. rhamnosus FS3051 and L. reuteri FS3052 inhibited N. seriolae, while B. subtilis natto NTU-18 did not inhibited N. seriolae. Probiotics also had the ability to secrete hydrolytic enzymes. Probiotic-fed grey mullet showed significant improvements in weight gain ratio, feed efficiency, and specific growth rate, particularly in the B. subtilis natto NTU-18 group. Immune gene expression was enhanced by probiotics, especially L. rhamnosus, FS3051, which induced IL-8, IL-1β, TNF-α, IFN-γ, and MHCI. Survival rates post-N. seriolae challenge improved significantly for L. rhamnosus FS3051-fed fish. L. rhamnosus FS3051 also altered the gut microbiota, enriching beneficial genera like Lactobacillus, which correlated positively with immune responses and growth, while reducing Mycoplasma and Rhodobacter, which were negatively correlated with immune responses. This study underscores the potential of probiotics in enhancing disease resistance and growth via regulating gut microbiota in grey mullet.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"67"},"PeriodicalIF":4.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes in social environment impact primate gut microbiota composition.","authors":"Colleen S Pearce, Danielle Bukovsky, Katya Douchant, Abhay Katoch, Jill Greenlaw, Daniel J Gale, Joseph Y Nashed, Don Brien, Valerie A Kuhlmeier, Mark A Sabbagh, Gunnar Blohm, Fernanda G De Felice, Martin Pare, Douglas J Cook, Stephen H Scott, Douglas P Munoz, Calvin P Sjaarda, Anita Tusche, Prameet M Sheth, Andrew Winterborn, Susan Boehnke, Jason P Gallivan","doi":"10.1186/s42523-024-00355-y","DOIUrl":"10.1186/s42523-024-00355-y","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet.</p><p><strong>Results: </strong>We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families - Lactobacillaceae and Clostridiaceae - demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet.</p><p><strong>Conclusions: </strong>Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"66"},"PeriodicalIF":4.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11562706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea.","authors":"Kelly J Stewart, Annette S Boerlage, William Barr, Umer Z Ijaz, Cindy J Smith","doi":"10.1186/s42523-024-00347-y","DOIUrl":"10.1186/s42523-024-00347-y","url":null,"abstract":"<p><strong>Background: </strong>Salmon aquaculture involves freshwater and seawater phases. Recently there has been an increase in multifactorial gill health challenges during the seawater phase which has led to an urgent need to understand the gill microbiome. There is a lack of understanding on what drives the composition of the gill microbiome, and the influence the freshwater stage has on its long-term composition. We characterise the gill microbiome from seven cohorts of Atlantic salmon raised in six different freshwater operational systems-recirculating aquaculture system (RAS), flowthrough (FT) and loch-based system, prior to and after transfer to seven seawater farms, over two different input seasons, S0 (2018) and S1 (2019).</p><p><strong>Results: </strong>Using the V1-V2 region of the 16S rRNA gene, we produced amplicon libraries absent of host contamination. We showed that hatchery system influenced the gill microbiome (PERMAOVA R² = 0.226, p < 0.001). Loch and FT systems were more similar to each other than the three RAS systems, which clustered together. On transfer to sea, the gill microbiomes of all fish changed and became more similar irrespective of the initial hatchery system, seawater farm location or season of input. Even though the gill microbiome among seawater farm locations were different between locations (PERMAOVA R² = 0.528, p < 0.001), a clustering of the gill microbiomes by hatchery system of origin was still observed 7-25 days after transfer (PERMAOVA R = 0.164, p < 0.001). Core microbiomes at genera level were observed among all fish in addition to freshwater only, and seawater only. At ASV level core microbiomes were observed among FT and loch freshwater systems only and among all seawater salmon. The gill microbiome and surrounding water at each hatchery had more shared ASVs than seawater farms.</p><p><strong>Conclusion: </strong>We showed hatchery system, loch, FT or RAS, significantly impacted the gill microbiome. On transfer to sea, the microbiomes changed and became more similar. After transfer, the individual sites to which the fish were transferred has a significant influence on microbiome composition, but interesting some clustering by hatchery system remained. Future gill disease mitigation methods that target enhancing the gill microbiome may be most effective in the freshwater stage, as there were more shared ASVs between water and gill at hatchery, compared to at sea.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"65"},"PeriodicalIF":4.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of gut microbiota in a generalist, golden snub-nosed monkey, adaptation to geographical diet change.","authors":"Yuhang Li, Yujie Yan, Haojie Wu, Yiyi Men, Yi Yang, Hengguang Fu, Derek Dunn, Xiaowei Wang, Genggeng Gao, Peng Zhang, Guixin Dong, Liyuan Hao, Jia Jia, Baoguo Li, Songtao Guo","doi":"10.1186/s42523-024-00349-w","DOIUrl":"10.1186/s42523-024-00349-w","url":null,"abstract":"<p><p>Changes in diet causing ecological stress pose a significant challenge to animal survival. In response, the gut microbiota, a crucial part of the host's digestive system, exhibits patterns of change reflective of alterations in the host's food component. The impact of temporal dietary shifts on gut microbiota has been elucidated through multidimensional modeling of both food component and macronutrient intake. However, the broad distribution of wild generalist and the intricate complexity of their food component hinder our capacity to ascertain the degree to which their gut microbiota assist in adapting to spatial dietary variations. We examined variation in patterns of the gut microbial community according to changes in diet and in a colobine monkey with a regional variable diet, the golden snub-nosed monkey (Rhinopithecus roxellana). Specifically, we analyse the interactions between variation in food component, macronutrient intake and the gut microbial community. We compared monkeys from four populations by quantifying food component and macronutrient intake, and by sequencing 16S rRNA and the microbial macro-genomes from the faecal samples of 44 individuals. We found significant differences in the diets and gut microbial compositions, in nutrient space and macronutrient intake among some populations. Variations in gut microbiota composition across distinct populations mirror the disparities in macronutrient intake, with a notable emphasis on carbohydrate. Geographical differences in the diet among of golden snub-nosed monkey populations will result in macronutrient intake variation, with corresponding differences in macronutrient intake driving regional differences in the compositions and abundances of gut microbiota. Importantly, the gut microbiota associated with core digestive functions does not vary, with the non-core gut microbiota fluctuating in response to variation in macronutrient intake. This characteristic may enable species heavily reliant on gut microbiota for digestion to adapt to diet changes. Our results further the understanding of the roles gut microbiota play in the formation of host dietary niches.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"63"},"PeriodicalIF":4.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diet affects reproductive development and microbiota composition in honey bees.","authors":"Anjali Zumkhawala-Cook, Patrick Gallagher, Kasie Raymann","doi":"10.1186/s42523-024-00350-3","DOIUrl":"10.1186/s42523-024-00350-3","url":null,"abstract":"<p><strong>Background: </strong>Gut microbes are important to the health and fitness of many animals. Many factors have been shown to affect gut microbial communities including diet, lifestyle, and age. Most animals have very complex physiologies, lifestyles, and microbiomes, making it virtually impossible to disentangle what factors have the largest impact on microbiota composition. Honeybees are an excellent model to study host-microbe interactions due to their relatively simple gut microbiota, experimental tractability, and eusociality. Worker honey bees have distinct gut microbiota from their queen mothers despite being close genetic relatives and living in the same environment. Queens and workers differ in numerous ways including development, physiology, pheromone production, diet, and behavior. In the prolonged absence of a queen or Queen Mandibular Pheromones (QMP), some but not all workers will develop ovaries and become \"queen-like\". Using this inducible developmental change, we aimed to determine if diet and/or reproductive development impacts the gut microbiota of honey bee workers.</p><p><strong>Results: </strong>Microbiota-depleted newly emerged workers were inoculated with a mixture of queen and worker gut homogenates and reared under four conditions varying in diet and pheromone exposure. Three weeks post-emergence, workers were evaluated for ovary development and their gut microbiota communities were characterized. The proportion of workers with developed ovaries was increased in the absence of QMP but also when fed a queen diet (royal jelly). Overall, we found that diet, rather than reproductive development or pheromone exposure, led to more \"queen-like\" microbiota in workers. However, we revealed that diet alone cannot explain the microbiota composition of workers.</p><p><strong>Conclusion: </strong>The hypothesis that reproductive development explains microbiota differences between queens and workers was rejected. We found evidence that diet is one of the main drivers of differences between the gut microbial community compositions of queens and workers but cannot fully explain the distinct microbiota of queens. Thus, we predict that behavioral and other physiological differences dictate microbiota composition in workers and queens. Our findings not only contribute to our understanding of the factors affecting the honey bee microbiota, which is important for bee health, but also illustrate the versatility and benefits of utilizing honeybees as a model system to study host-microbe interactions.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"64"},"PeriodicalIF":4.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11539837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea.","authors":"C Prioux, C Ferrier-Pages, J Deter, R Tignat-Perrier, A Guilbert, L Ballesta, D Allemand, J A J M van de Water","doi":"10.1186/s42523-024-00351-2","DOIUrl":"10.1186/s42523-024-00351-2","url":null,"abstract":"<p><strong>Background: </strong>Corals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals.</p><p><strong>Results: </strong>16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns.</p><p><strong>Conclusions: </strong>Overall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"62"},"PeriodicalIF":4.9,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Programming rumen microbiome development in calves with the anti-methanogenic compound 3-NOP.","authors":"Gonzalo Martinez-Fernandez, Stuart E Denman, Nicola Walker, Maik Kindermann, Christopher S McSweeney","doi":"10.1186/s42523-024-00343-2","DOIUrl":"10.1186/s42523-024-00343-2","url":null,"abstract":"<p><p>The aim of this study was to establish a distinctive rumen microbial and fermentation profile using the anti-methanogenic compound 3-NOP to assess dam effect, and nutritional intervention of the juvenile offspring on microbial structure and function of rumen up to 12 months of age, once the treatment was withdrawn. Forty-eight pregnant heifers (H) and their future offspring (C) were allocated to either Control (-) or 3-NOP (+) treatment resulting in four experimental groups: H+/C+, H+/C-, H-/C + and H-/C-. Animals were treated from 6 weeks prior to calving until weaning, with the offspring monitored until 12 months of age. Rumen fluid samples and methane measurements using the Greenfeed system were collected during the trial. Results supported the mode of action of the compound, with a shift in fermentation from acetate to propionate, increases in branched chain fatty acids and formic acid in the 3-NOP treated animals. Similar shifts in microbial populations occurred in 3-NOP treated animals with lower abundances of rumen methanogen populations, increases of bacterial groups Succiniclasticum spp, Candidatus Saccharimonas. Fibrobacter and the families Prevotellaceae and Succinivibrioacea. and the protozoa Entodinium. Early life intervention had an enduring impact on the rumen microbial structure of young animals up to 28 weeks post weaning, however the effect was diminished once 3-NOP was withdrawn. Interestingly, a group of young animals emitted significantly less methane (15%) than the animals that did not receive the treatment during their juvenile stage. Our results suggest a higher resemblance of the young calf microbiome to a low methane adult and that early life colonisation of the rumen persists through to later life with the pre-weaning microbiome comprising ~ 65% of the yearling animal. Further research needs to be performed to determine the timing and dose of 3-NOP for new-born calves that can sustain a reduction in methane emissions after the treatment is withdrawn, under extensive grazing or controlled conditions.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"60"},"PeriodicalIF":4.9,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement.","authors":"Abimael Ortiz-Chura, Milka Popova, Diego P Morgavi","doi":"10.1186/s42523-024-00348-x","DOIUrl":"10.1186/s42523-024-00348-x","url":null,"abstract":"<p><p>The ruminant microbiome plays a key role in the health, feed utilization and environmental impact of ruminant production systems. Microbiome research provides insights to reduce the environmental footprint and improve meat and milk production from ruminants. However, the microbiome composition depends on the ruminant species, habitat and diet, highlighting the importance of having a good representation of ruminant microbiomes in their local environment to translate research findings into beneficial approaches. This information is currently lacking. In this study, we examined the metadata of farmed ruminant microbiome studies to determine global representativeness and summarized information by ruminant species, geographic location, body site, and host information. We accessed data from the International Nucleotide Sequence Database Collaboration via the National Center for Biotechnology Information database. We retrieved 47,628 sample metadata, with cattle accounting for more than two-thirds of the samples. In contrast, goats, which have a similar global population to cattle, were underrepresented with less than 4% of the total samples. Most samples originated in Western Europe, North America, Australasia and China but countries with large ruminant populations in South America, Africa, Asia, and Eastern Europe were underrepresented. Microbiomes from the gastrointestinal tract were the most frequently studied, comprising about 87% of all samples. Additionally, the number of samples from other body sites such as the respiratory tract, milk, skin, reproductive tract, and fetal tissue, has markedly increased over the past decade. More than 40% of the samples lacked basic information and many were retrieved from generic taxonomic classifications where the ruminant species was manually recovered. The lack of basic information such as age, breed or sex can limit the reusability of the data for further analysis and follow-up studies. This requires correct taxonomic assignment of the ruminant host and basic metadata information using accepted ontologies adapted to host-associated microbiomes. Repositories should require this information as a condition of acceptance. The results of this survey highlight the need to encourage studies of the ruminant microbiome from underrepresented ruminant species and countries worldwide. This shortfall in information poses a challenge for the development of microbiome-based strategies to meet sustainability requirements, particularly in areas with expanding livestock production systems.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"61"},"PeriodicalIF":4.9,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary β-mannanase reduced post-weaning diarrhea of pigs by positively modulating gut microbiota and attenuating systemic immune responses.","authors":"Ki Beom Jang, Yonghee Kim, Jinmu Ahn, Jae In Lee, Sangwoo Park, Jeehwan Choe, Younghoon Kim, Jae Hwan Lee, Hyunjin Kyoung, Minho Song","doi":"10.1186/s42523-024-00346-z","DOIUrl":"10.1186/s42523-024-00346-z","url":null,"abstract":"<p><strong>Background: </strong>After weaning, nursery pigs have difficulty digesting non-starch polysaccharides in their diets, which can result in growth and health problems. Among non-starch polysaccharides, β-mannan is easily found in various cereal grains that form the basis of livestock diets and interferes the digestion and utilization of nutrients. Supplementation of dietary β-mannanase in nursery diet can alleviate the negative effects on nutrient utilization efficiency caused by β-mannan and improve growth and health of pigs. This study was conducted to evaluate effects of dietary β-mannanase supplementation on growth performance, nutrient digestibility, intestinal morphology, fecal microbiota, and systemic immune responses of weaned pigs.</p><p><strong>Results: </strong>Dietary β-mannanase (MAN) improved average daily gain (P = 0.053), average daily feed intake (P < 0.05), and gain to feed ratio (P = 0.077) of pigs for 3 weeks after weaning and apparent total tract digestibility of crude protein (P = 0.060) and reduced post-weaning diarrhea (P < 0.05). The MAN did not affect the ileal morphology. Pigs fed with MAN had more diverse fecal microbiota based on the results of alpha diversity [the number of operational taxonomic units (OTUs; P = 0.061), Shannon (P = 0.071), and Simpson indices (P = 0.078)] and relative abundance of phylum Bacteroidetes (P = 0.064) and genus Prevotella (P < 0.05) than pigs fed control diet (CON). As a result of beta diversity, fecal microbiota was clustered (P < 0.05) into two distinct groups between dietary treatments. The MAN decreased (P < 0.05) packed cell volume (PCV), the number of white blood cells (WBC), C-reactive protein (CRP), tumor necrosis factor-α (TNF-α), transforming growth factor-β1 (TGF-β1), and cortisol of the pigs for 2 weeks after weaning compared with CON.</p><p><strong>Conclusion: </strong>Dietary β-mannanase reduced post-weaning diarrhea of pigs by positively modulating gut microbiota and attenuating systemic immune responses.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"59"},"PeriodicalIF":4.9,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}