Animal microbiome最新文献

{"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}

{"title":"Unravelling the complexity of bovine milk microbiome: insights into mastitis through enterotyping using full-length 16S-metabarcoding.","authors":"Leire Urrutia-Angulo, Medelin Ocejo, Beatriz Oporto, Gorka Aduriz, José Luís Lavín, Ana Hurtado","doi":"10.1186/s42523-024-00345-0","DOIUrl":"10.1186/s42523-024-00345-0","url":null,"abstract":"<p><strong>Background: </strong>Mastitis, inflammation of the mammary gland, is a major disease of dairy cattle and the main cause for antimicrobial use. Although mainly caused by bacterial infections, the aetiological agent often remains unidentified by conventional microbiological culture methods. The aim of this study was to test whether shifts in the bovine mammary gland microbiota can result in initiation or progression of mastitis.</p><p><strong>Methods: </strong>Oxford-Nanopore long-read sequencing was used to generate full-length 16S rRNA gene reads (16S-metabarcoding) to characterise the microbial population of milk from healthy and diseased udder of cows classified into five groups based on their mastitis history and parity.</p><p><strong>Results: </strong>Samples were classified into six enterotypes, each characterised by a marker genus and several differentially-abundant genera. Two enterotypes were exclusively composed of clinical mastitis samples and displayed a marked dysbiosis, with a single pathogenic genus predominating and displacing the endogenous bacterial population. Other mastitis samples (all subclinical and half of the clinical) clustered with those from healthy animals into three enterotypes, probably reflecting intermediate states between health and disease. After an episode of clinical mastitis, clinical recovery and microbiome reconstitution do not always occur in parallel, indicating that the clinical definition of the udder health status does not consistently reflect the microbial profile.</p><p><strong>Conclusions: </strong>These results show that mastitis is a dynamic process in which the udder microbiota constantly changes, highlighting the complexity of defining a unique microbiota profile indicative of mastitis.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"58"},"PeriodicalIF":4.9,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513968","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":"Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout.","authors":"Guglielmo Raymo, Fabiane Januario, Ali Ali, Ridwan O Ahmed, Rafet Al-Tobasei, Mohamed Salem","doi":"10.1186/s42523-024-00344-1","DOIUrl":"https://doi.org/10.1186/s42523-024-00344-1","url":null,"abstract":"<p><strong>Background: </strong>Recirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.</p><p><strong>Results: </strong>The moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.</p><p><strong>Conclusion: </strong>Our study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"57"},"PeriodicalIF":4.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11484228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482196","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":"Genetics, age, and diet influence gut bacterial communities and performance of black soldier fly larvae (Hermetia illucens).","authors":"Shaktheeshwari Silvaraju, Qi-Hui Zhang, Sandra Kittelmann, Nalini Puniamoorthy","doi":"10.1186/s42523-024-00340-5","DOIUrl":"https://doi.org/10.1186/s42523-024-00340-5","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota of black soldier fly larvae (BSFL, Hermetia illucens) play a crucial role in recycling various organic waste streams. This capability is linked to the presence of a potential common core microbiota in BSFL. However, subjective thresholds for defining core taxa and the difficulty of separating genetic and environmental influences have prevented a clear consensus in the literature. We analysed the gut bacterial communities of two genetically distinct BSF lines (wild type (WT) and lab-adapted line (LD)) raised on ten different diets based on common agricultural by-products and food waste in Southeast Asia.</p><p><strong>Results: </strong>High-throughput 16S rRNA gene sequencing revealed that gut bacterial communities were significantly influenced by genetics (p = 0.001), diet (plant/meat-dominated; p = 0.001), larval age (p = 0.001), and the interactions between all three (p = 0.002). This led us to investigate both common core taxa and lineage-specific core taxa. At a strict > 97% prevalence threshold, four core taxa were identified: Providencia_A_732258, an unclassified genus within the family Enterococcaceae, Morganella, and Enterococcus_H_360604. A relaxed threshold (> 80% prevalence) extended the core to include other potential common core taxa such as Klebsiella, Proteus, and Scrofimicrobium. Our data suggest that Proteus, Scrofimicrobium, Corynebacterium, Vagococcus_B, Lysinibacillus_304693 (all LD), and Paenibacillus_J_366884 (WT) are lineage-specific rather than members of a common core (> 90% prevalence in either LD or WT, with prevalence significantly different between lines (p ≤ 0.05)). Positive correlations were observed between several core genera and larval performance in LD, typical of a highly optimized lab-adapted line. Interestingly, only members of the genus Providencia appeared to play a crucial role in most aspects of larval performance in both genetic lineages.</p><p><strong>Conclusion: </strong>Our study demonstrates that the gut microbiota of BSFL is influenced by genetic factors, diet composition, larval age, and their interactions. We identified a distinct lineage-specific core microbiota, emphasizing genetic background's role. Future studies should apply a standardized high prevalence threshold of at least > 90% unless there is a valid reason for relaxation or sample exclusion. The consistent association of Providencia spp. with larval performance across both genetic lines highlights their crucial role in the BSFL gut ecosystem.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"56"},"PeriodicalIF":4.9,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482197","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":"Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community.","authors":"Elena Bollati, David J Hughes, David J Suggett, Jean-Baptiste Raina, Michael Kühl","doi":"10.1186/s42523-024-00341-4","DOIUrl":"https://doi.org/10.1186/s42523-024-00341-4","url":null,"abstract":"<p><p>Animal guts contain numerous microbes, which are critical for nutrient assimilation and pathogen defence. While corals and other Cnidaria lack a true differentiated gut, they possess semi-enclosed gastrovascular cavities (GVCs), where vital processes such as digestion, reproduction and symbiotic exchanges take place. The microbiome harboured in GVCs is therefore likely key to holobiont fitness, but remains severely understudied due to challenges of working in these small compartments. Here, we developed minimally invasive methodologies to sample the GVC of coral polyps and characterise the microbial communities harboured within. We used glass capillaries, low dead volume microneedles, or nylon microswabs to sample the gastrovascular microbiome of individual polyps from six species of corals, then applied low-input DNA extraction to characterise the microbial communities from these microliter volume samples. Microsensor measurements of GVCs revealed anoxic or hypoxic micro-niches, which persist even under prolonged illumination with saturating irradiance. These niches harboured microbial communities enriched in putatively microaerophilic or facultatively anaerobic taxa, such as Epsilonproteobacteria. Some core taxa found in the GVC of Lobophyllia hemprichii from the Great Barrier Reef were also detected in conspecific colonies held in aquaria, indicating that these associations are unlikely to be transient. Our findings suggest that the coral GVC is chemically and microbiologically similar to the gut of higher Metazoa. Given the importance of gut microbiomes in mediating animal health, harnessing the coral \"gut microbiome\" may foster novel active interventions aimed at increasing the resilience of coral reefs to the climate crisis.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"55"},"PeriodicalIF":4.9,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395676","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 modulation of intestinal commensal bacteria possibly contributes to the growth and immunity promotion in Epinephelus akaara after feeding the antimicrobial peptide Scy-hepc.","authors":"Hang Sun, Luxi Wang, Fangyi Chen, Xiangyu Meng, Wenbin Zheng, Hui Peng, Hua Hao, Huiyun Chen, Ke-Jian Wang","doi":"10.1186/s42523-024-00342-3","DOIUrl":"https://doi.org/10.1186/s42523-024-00342-3","url":null,"abstract":"<p><strong>Background: </strong>Our previous study revealed that feeding the antimicrobial peptide (AMP) product Scy-hepc significantly enhances the growth of mariculture fish through the activation of the GH-Jak2-STAT5-IGF1 axis. However, the contribution of gut microbiota to this growth enhancement remains unclear. This study aimed to elucidate the potential mechanism involved in intestinal absorption and modulation of gut microbiota in Epinephelus akaara following Scy-hepc feeding.</p><p><strong>Results: </strong>The results showed that a 35 day regimen of Scy-hpec markedly promoted the growth of E. akaara compared to groups supplemented with either florfenicol, B. subtilis, or a vector. The growth enhancement is likely attributed to alterations in microbiota colonization in the foregut and midgut, characterized by an increasing abundance of potential probiotics (Rhizobiaceae and Lysobacter) and a decreased abundance of opportunistic pathogens (Psychrobacter and Brevundimonas) as determined by 16S rRNA analysis. Additionally, similar to the effect of florfenicol feeding, Scy-hepc significantly improved host survival rate by over 20% in response to a lethal dose challenge with Edwardsiella tarda. Further investigations demonstrated that Scy-hepc is absorbed by the fish foregut (20-40 min) and midgut (20-30 min) as confirmed by Western blot, ELISA, and Immunofluorescence. The absorption of Scy-hepc affected the swimming, swarming and surfing motility of Vibrio harveyi and Bacillus thuringiensis isolated from E. akaara's gut. Moreover, Scy-hepc induced the downregulation of 40 assembly genes and the upregulation expression of 5, with the most significant divergence in gene expression between opportunistic pathogens and probiotics concentrated in their motility genes (PomA/B, MotA/B).</p><p><strong>Conclusions: </strong>In summary, this study shows that feeding AMP Scy-hepc can promote growth and bolster immunity in E. akaara. These beneficial effects are likely due to the absorption of Scy-hepc in the fish's foregut and midgut, which modulates the colonization and motility of commensal bacteria, leading to favorable changes in the composition of the foregut and midgut microbiota. Therefore, a profound understanding of the mechanisms by which antimicrobial peptides affect host gut microbiota will contribute to a comprehensive assessment of their advantages and potential application prospects as substitutes for antibiotics in fish health and improving aquaculture practices.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"54"},"PeriodicalIF":4.9,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11459891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395677","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":"Microbiome signature suggestive of lactose-intolerance in rhesus macaques (Macaca mulatta) with intermittent chronic diarrhea.","authors":"Annemiek Maaskant, Bas Voermans, Evgeni Levin, Marcus C de Goffau, Nicole Plomp, Frank Schuren, Edmond J Remarque, Antoine Smits, Jan A M Langermans, Jaco Bakker, Roy Montijn","doi":"10.1186/s42523-024-00338-z","DOIUrl":"10.1186/s42523-024-00338-z","url":null,"abstract":"<p><strong>Background: </strong>Chronic diarrhea is a common cause of mortality and morbidity in captive rhesus macaques (Macaca mulatta). The exact etiology of chronic diarrhea in macaques remains unidentified. The occurrence of diarrhea is frequently linked to dysbiosis within the gut microbiome. Research into microbiome signatures correlated with diarrhea in macaques have predominantly been conducted with single sample collections. Our analysis was based on the metagenomic composition of longitudinally acquired fecal samples from rhesus macaques with chronic diarrhea and clinically healthy rhesus macaques that were obtained over the course of two years. We aimed to investigate potential relationships between the macaque gut microbiome, the presence of diarrhea and diet interventions with a selection of commercially available monkey diets.</p><p><strong>Results: </strong>The microbiome signature of macaques with intermittent chronic diarrhea showed a significant increase in lactate producing bacteria e.g. lactobacilli, and an increase in fermenters of lactate and succinate. Strikingly, two lactose free diets were associated with a lower incidence of diarrhea.</p><p><strong>Conclusion: </strong>A lactose intolerance mechanism is suggested in these animals by the bloom of Lactobacillus in the presence of lactose resulting in an overproduction of intermediate fermentation products likely led to osmotically induced diarrhea. This study provides new insights into suspected microbiome-lactose intolerance relationship in rhesus macaques with intermittent chronic diarrhea. The integration of machine learning with metagenomic data analysis holds potential for developing targeted dietary interventions and therapeutic strategies and therefore ensuring a healthier and more resilient primate population.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"53"},"PeriodicalIF":4.9,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309230","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":"Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiency.","authors":"Kate Keogh, David A Kenny, Pamela A Alexandre, Sinead M Waters, Emily McGovern, Mark McGee, Antonio Reverter","doi":"10.1186/s42523-024-00337-0","DOIUrl":"https://doi.org/10.1186/s42523-024-00337-0","url":null,"abstract":"<p><strong>Background: </strong>Feed costs account for a high proportion of the variable cost of beef production, ultimately impacting overall profitability. Thus, improving feed efficiency of beef cattle, by way of determining the underlying genomic control and selecting for feed efficient cattle provides a method through which feed input costs may be reduced whilst also contributing to the environmental sustainability of beef production. The rumen microbiome dictates the feed degradation capacity and consequent nutrient supply in ruminants, thus potentially impacted by feed efficiency phenotype. Equally, liver tissue has been shown to be responsive to feed efficiency phenotype as well as dietary intake. However, although both the rumen microbiome and liver transcriptome have been shown to be impacted by host feed efficiency phenotype, knowledge of the interaction between the rumen microbiome and other peripheral tissues within the body, including the liver is lacking. Thus, the objective of this study was to compare two contrasting breed types (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI) over contrasting dietary phases (zero-grazed grass and high-concentrate), based on gene co-expression network analysis of liver transcriptome data and microbe co-abundance network of rumen microbiome data. Traits including RFI, dry matter intake (DMI) and growth rate (ADG), as well as rumen concentrations of volatile fatty acids were also included within the network analysis.</p><p><strong>Results: </strong>Overall, DMI had the greatest number of connections followed by RFI, with ADG displaying the fewest number of significant connections. Hepatic genes related to lipid metabolism were correlated to both RFI and DMI phenotypes, whilst genes related to immune response were correlated to DMI. Despite the known relationship between RFI and DMI, the same microbes were not directly connected to these phenotypes, the Succiniclasticum genus was however, negatively connected to both RFI and ADG. Additionally, a stepwise regression analysis revealed significant roles for both Succiniclasticum genus and Roseburia.faecis sp. in predicting RFI, DMI and ADG.</p><p><strong>Conclusions: </strong>Results from this study highlight the interactive relationships between rumen microbiome and hepatic transcriptome data of cattle divergent for RFI, whilst also increasing our understanding of the underlying biology of both DMI and ADG in beef cattle.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"52"},"PeriodicalIF":4.9,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11414306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302260","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 early life microbiome of giant grouper (Epinephelus lanceolatus) larvae in a commercial hatchery is influenced by microorganisms in feed.","authors":"Jin Yan Lim, Yun Kit Yeoh, Maximiliano Canepa, Richard Knuckey, Dean R Jerry, David G Bourne","doi":"10.1186/s42523-024-00339-y","DOIUrl":"https://doi.org/10.1186/s42523-024-00339-y","url":null,"abstract":"<p><p>Fish health, growth and disease is intricately linked to its associated microbiome. Understanding the influence, source and ultimately managing the microbiome, particularly for vulnerable early life-stages, has been identified as one of the key requirements to improving farmed fish production. One tropical fish species of aquaculture importance farmed throughout the Asia-Pacific region is the giant grouper (Epinephelus lanceolatus). Variability in the health and survival of E. lanceolatus larvae is partially dependent on exposure to and development of its early microbiome. Here, we examined the development in the microbiome of commercially reared giant grouper larvae, its surrounding environment, and that from live food sources to understand the type of bacterial species larvae are exposed to, and where some of the sources of bacteria may originate. We show that species richness and microbial diversity of the larval microbiome significantly increased in the first 4 days after hatching, with the community composition continuing to shift over the initial 10 days in the hatchery facility. The dominant larval bacterial taxa appeared to be predominantly derived from live cultured microalgae and rotifer feeds and included Marixanthomonas, Candidatus Hepatincola, Meridianimaribacter and Vibrio. In contrast, a commercial probiotic added as part of the hatchery's operating procedure failed to establish in the larvae microbiome. Microbial source tracking indicated that feed was the largest influence on the composition of the giant grouper larvae microbiome (up to 55.9%), supporting attempts to modulate fish microbiomes in commercial hatcheries through improved diets. The marked abundances of Vibrio (up to 21.7% of 16S rRNA gene copies in larvae) highlights a need for rigorous quality control of feed material.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"51"},"PeriodicalIF":4.9,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302261","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}