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Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. 南方狨猴(Tamandua tetradactyla)的微生物组组成和可培养共生群的存在随圈养条件而变化。
Q1 MICROBIOLOGY Pub Date : 2024-05-02 DOI: 10.1186/s42523-024-00311-w
Ahmad Amin, Chahrazed Mekadim, Nikol Modrackova, Petra Bolechova, Jakub Mrazek, Vera Neuzil-Bunesova

Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.

南方狨(Tamandua tetradactyla)属于专门的胎盘栉水母。关于它们肠道微生物群的信息并不多。此外,由于它们的食物专一性,很难在饲养条件下提供充足的食物。因此,我们使用 16S rDNA 扩增子测序法分析了捷克共和国四个地方圈养的南方狨猴的粪便微生物组,并评估了进食和设施条件对微生物组组成的影响。在进行微生物组分析的同时,我们还对可培养的共生动物进行了量化和鉴定。食蚁兽粪便微生物组以芽孢杆菌科(Bacillota)和类杆菌科(Bacteroidota)为主,而假单胞菌科(Pseudomonadota)、螺旋体科(Spirochaetota)和放线菌科(Actinobacteriota)的数量较少。在分类学科一级,所有地点的动物粪便微生物组中主要有乳酸菌科(Lachnospiraceae)、前鞭毛菌科(Prevotellaceae)、类杆菌科(Bacteroidaceae)、震旦菌科(Oscillospiraceae)、酵母菌科(Erysipelotrichaceae)、螺旋藻科(Spirochaetaceae)、反刍球菌科(Ruminococcaceae)、亮球菌科(Leuconostocaceae)和链球菌科(Streptococcaceae)。有趣的是,乳酸菌科在动物园食谱中占主导地位。这些动物的肠道微生物组多样性也明显低于其他地点主要以全价商品饲料喂养的动物。此外,被分析食蚁兽的圈养条件还包括其他一些因素,如在食物中添加昆虫产品、益生菌干预、接触其他动物等,这些因素都可能影响微生物组的组成和可培养的微生物。利用 MALDI-TOF MS 技术,从一千多个精选分离物中分离并鉴定了从有益共生菌到机会性病原体的 63 种细菌。检测到的物种中有一半存在于大多数动物的粪便微生物群中,其余物种则因动物和地点而异。
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引用次数: 0
Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment. 猪场和周围环境中抗菌细菌的散布。
Q1 MICROBIOLOGY Pub Date : 2024-03-30 DOI: 10.1186/s42523-024-00305-8
Daniel Scicchitano, Daniela Leuzzi, Giulia Babbi, Giorgia Palladino, Silvia Turroni, Cédric Christian Laczny, Paul Wilmes, Federico Correa, Pimlapas Leekitcharoenphon, Castrense Savojardo, Diana Luise, Pierluigi Martelli, Paolo Trevisi, Frank Møller Aarestrup, Marco Candela, Simone Rampelli

Background: Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment.

Results: In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe.

Conclusions: Collectively, our results highlight the urgency to implement more effective countermeasures to limit the dispersion of ARGs in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems.

背景:抗菌药耐药性已被认为是对全球健康的一大威胁。猪的食物链被认为是抗菌药耐药性基因(ARGs)的重要来源。然而,人们对 ARGs 在养猪生产系统(包括外部环境)中的散布情况仍然缺乏了解:在本研究中,我们对位于意大利的一个猪场进行了从断奶期到屠宰场的纵向跟踪,以全面评估 ARGs 的多样性、扩散情况以及与之相关的细菌。我们从 294 个样本(包括猪粪便、猪场环境、猪场周围土壤、废水和屠宰场环境)中获得了猎枪元基因组序列。我们共鉴定出 530 个物种级基因组区(SGB),从而评估了养殖系统中微生物及其相关 ARGs 的扩散情况。我们在动物肠道微生物组、农场内部和外部环境之间发现了 309 个共享的 SGBs。具体来说,这些 SGBs 的特点是抗药性组多样而复杂,其 ARGs 对 18 种不同类别的抗生素化合物具有活性,这与欧洲猪食物链中抗生素的使用情况完全吻合:总之,我们的研究结果突出表明,迫切需要采取更有效的应对措施来限制 ARGs 在猪食品系统中的扩散,同时,基于元基因组学的方法对 ARGs 的扩散进行监测对猪场工作环境和周围生态系统的安全具有重要意义。
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引用次数: 0
Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota. 探索森林城市化对小型哺乳动物群落及其肠道微生物群之间相互作用的潜在影响。
Q1 MICROBIOLOGY Pub Date : 2024-03-25 DOI: 10.1186/s42523-024-00301-y
Marie Bouilloud, Maxime Galan, Julien Pradel, Anne Loiseau, Julien Ferrero, Romain Gallet, Benjamin Roche, Nathalie Charbonnel

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

城市化极大地影响了野生种群,使城市居民物种优于那些无法适应快速变化的物种。这些不同的适应能力可能是由微生物组介导的,微生物组可以通过高度的灵活性迅速调节宿主的表型。反之,在人类活动的干扰下,一些物种的微生物群可能会受到破坏,导致菌群失调,对宿主的健康产生负面影响。城市化对宿主群落的影响与宿主肠道微生物群(GM)之间的联系还很少有人探讨。在这项研究中,我们检验了一个假设,即肠道微生物群的细菌组成可能在宿主适应城市环境中发挥作用。我们采用 16S 代谢编码方法,描述了沿城市化梯度在森林地区采样的几种小型陆生哺乳动物的基因组。考虑到细菌类群的存在和丰度及其可能的功能,我们测试了城市化是否导致小型哺乳动物群落及其基因组的变化。这有助于破译这些变化背后的过程。我们发现了城市化对小型哺乳动物群落及其基因改造的潜在影响。与城市适配物种相比,城市居民物种的细菌分类多样性较低,但功能多样性较高,组成也不同。它们的基因组组装主要受随机效应的影响,可能表明菌群失调。尽管存在菌群失调现象,但仍检测到了与适应城市环境有关的选择过程和过多的功能。在城市适配物种中,基因组功能多样性和组成在城市化梯度上保持相对稳定。这一现象可以用功能冗余来解释,即某些类群表达相同的功能。这可能有利于城市适配物种适应各种环境,包括城市环境。因此,我们可以假定,在群落中,肠道微生物群与宿主物种之间存在反馈,从而实现快速适应。
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引用次数: 0
Correction: Dietary Bacillus spp. supplementation to both sow and progenies improved post-weaning growth rate, gut function, and reduce the pro-inflammatory cytokine production in weaners challenged with Escherichia coli K88. 更正:母猪和后代膳食中添加枯草芽孢杆菌可提高断奶后的生长速度和肠道功能,并减少断奶仔猪受到大肠杆菌 K88 挑战时产生的促炎细胞因子。
Q1 MICROBIOLOGY Pub Date : 2024-03-19 DOI: 10.1186/s42523-024-00302-x
Vetriselvi Sampath, Sungbo Cho, Jinuk Jeong, Seyoung Mun, Choon Han Lee, Rafael Gustavo Hermes, Apichaya Taechavasonyoo, Natasja Smeets, Susanne Kirwan, Kyudong Han, In Ho Kim
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引用次数: 0
Dietary L-Methionine modulates the gut microbiota and improves the expression of tight junctions in an in vitro model of the chicken gastrointestinal tract. 在鸡胃肠道体外模型中,膳食 L-蛋氨酸可调节肠道微生物群并改善紧密连接的表达。
IF 4.9 Q1 MICROBIOLOGY Pub Date : 2024-03-19 DOI: 10.1186/s42523-024-00303-w
Min-Jin Kwak, Anna Kang, JuYoung Eor, Sangdon Ryu, Youbin Choi, Jung Min Heo, Minho Song, Jong Nam Kim, Hyeon-Jin Kim, Younghoon Kim

Background: The poultry industry encounters a number of factors that affect growth performance and productivity; nutrition is essential for sustaining physiological status and protecting against stressors such as heat, density, and disease. The addition of vitamins, minerals, and amino acids to the diet can help restore productivity and support the body's defense mechanisms against stress. Methionine (Met) is indispensable for poultry's energy metabolism, physiology, performance, and feed utilization capacity. Through this study, we aimed to examine the physiological effects of methionine supplementation on poultry as well as alterations of intestinal microbiome.

Methods: We utilized the DL- and L- form of methionine on Caenorhabditis elegans and the FIMM (Fermentor for intestine microbiota model) in-vitro digesting system. A genomic-analysis of the transcriptome confirmed that methionine supplementation can modulate growth-related physiological metabolic pathways and immune responses in the host poultry. The C. elegans model was used to assess the general health benefits of a methionine supplement for the host.

Results: Regardless of the type or concentration of methionine, supplementation with methionine significantly increased the lifespan of C. elegans. Feed grade L-Methionine 95%, exhibited the highest lifespan performance in C. elegans. Methionine supplementation increased the expression of tight junction genes in the primary intestinal cells of both broiler and laying hens, which is directly related to immunity. Feed grade L-Methionine 95% performed similarly or even better than DL-Methionine or L-Methionine treatments with upper doses in terms of enhancing intestinal integrity. In vitro microbial cultures of healthy broilers and laying hens fed methionine revealed changes in intestinal microflora, including increased Clostridium, Bacteroides, and Oscillospira compositions. When laying hens were given feed grade L-Methionine 95% and 100%, pathogenic Campylobacter at the genus level was decreased, while commensal bacteria were increased.

Conclusions: Supplementation of feed grade L-Methionine, particularly L-Methionine 95%, was more beneficial to the host poultry than supplementing other source of methionine for maintaining intestinal integrity and healthy microbiome.

背景:家禽业会遇到许多影响生长性能和生产率的因素;营养对于维持生理状态和抵御热、密度和疾病等应激因素至关重要。在日粮中添加维生素、矿物质和氨基酸有助于恢复生产性能,并支持机体的防御机制抵御应激。蛋氨酸(Met)对家禽的能量代谢、生理机能、生产性能和饲料利用能力都是不可或缺的。本研究旨在探讨补充蛋氨酸对家禽的生理影响以及肠道微生物组的改变:方法:我们利用 DL 型和 L 型蛋氨酸对秀丽隐杆线虫和 FIMM(肠道微生物群发酵剂模型)体外消化系统进行了研究。转录组的基因组分析证实,补充蛋氨酸可调节宿主家禽与生长相关的生理代谢途径和免疫反应。利用秀丽隐杆线虫模型来评估补充蛋氨酸对宿主健康的总体益处:结果:无论蛋氨酸的类型或浓度如何,补充蛋氨酸都能显著延长秀丽隐杆线虫的寿命。饲料级 L-蛋氨酸含量为 95%,对 elegans 的寿命影响最大。补充蛋氨酸可增加肉鸡和蛋鸡肠道原代细胞中紧密连接基因的表达,这与免疫力直接相关。在增强肠道完整性方面,饲料级 L-Methionine 95% 的表现与 DL-Methionine 或高剂量 L-Methionine 处理相似,甚至更好。对饲喂蛋氨酸的健康肉鸡和蛋鸡进行体外微生物培养发现,肠道微生物区系发生了变化,包括梭状芽孢杆菌、嗜酸乳杆菌和震旦梭菌成分增加。当蛋鸡摄入 95% 和 100% 的饲料级 L-蛋氨酸时,致病弯曲杆菌属水平下降,而共生菌增加:补充饲料级 L-蛋氨酸(尤其是 95%的 L-蛋氨酸)比补充其他来源的蛋氨酸更有利于家禽保持肠道完整性和健康的微生物群。
{"title":"Dietary L-Methionine modulates the gut microbiota and improves the expression of tight junctions in an in vitro model of the chicken gastrointestinal tract.","authors":"Min-Jin Kwak, Anna Kang, JuYoung Eor, Sangdon Ryu, Youbin Choi, Jung Min Heo, Minho Song, Jong Nam Kim, Hyeon-Jin Kim, Younghoon Kim","doi":"10.1186/s42523-024-00303-w","DOIUrl":"10.1186/s42523-024-00303-w","url":null,"abstract":"<p><strong>Background: </strong>The poultry industry encounters a number of factors that affect growth performance and productivity; nutrition is essential for sustaining physiological status and protecting against stressors such as heat, density, and disease. The addition of vitamins, minerals, and amino acids to the diet can help restore productivity and support the body's defense mechanisms against stress. Methionine (Met) is indispensable for poultry's energy metabolism, physiology, performance, and feed utilization capacity. Through this study, we aimed to examine the physiological effects of methionine supplementation on poultry as well as alterations of intestinal microbiome.</p><p><strong>Methods: </strong>We utilized the DL- and L- form of methionine on Caenorhabditis elegans and the FIMM (Fermentor for intestine microbiota model) in-vitro digesting system. A genomic-analysis of the transcriptome confirmed that methionine supplementation can modulate growth-related physiological metabolic pathways and immune responses in the host poultry. The C. elegans model was used to assess the general health benefits of a methionine supplement for the host.</p><p><strong>Results: </strong>Regardless of the type or concentration of methionine, supplementation with methionine significantly increased the lifespan of C. elegans. Feed grade L-Methionine 95%, exhibited the highest lifespan performance in C. elegans. Methionine supplementation increased the expression of tight junction genes in the primary intestinal cells of both broiler and laying hens, which is directly related to immunity. Feed grade L-Methionine 95% performed similarly or even better than DL-Methionine or L-Methionine treatments with upper doses in terms of enhancing intestinal integrity. In vitro microbial cultures of healthy broilers and laying hens fed methionine revealed changes in intestinal microflora, including increased Clostridium, Bacteroides, and Oscillospira compositions. When laying hens were given feed grade L-Methionine 95% and 100%, pathogenic Campylobacter at the genus level was decreased, while commensal bacteria were increased.</p><p><strong>Conclusions: </strong>Supplementation of feed grade L-Methionine, particularly L-Methionine 95%, was more beneficial to the host poultry than supplementing other source of methionine for maintaining intestinal integrity and healthy microbiome.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"14"},"PeriodicalIF":4.9,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10953145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140178040","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}
引用次数: 0
Enhancing seafood traceability: tracking the origin of seabass and seabream from the tuscan coast area by the analysis of the gill bacterial communities. 提高海产品的可追溯性:通过分析鳃细菌群落追踪托斯卡纳海岸地区鲈鱼和鲷鱼的产地。
Q1 MICROBIOLOGY Pub Date : 2024-03-14 DOI: 10.1186/s42523-024-00300-z
Niccolò Meriggi, Alessandro Russo, Sonia Renzi, Benedetta Cerasuolo, Marta Nerini, Alberto Ugolini, Massimiliano Marvasi, Duccio Cavalieri

Background: The seafood consumption and trade have increased over the years, and along its expected expansion pose major challenges to the seafood industry and government institutions. In particular, the global trade in fish products and the consequent consumption are linked to reliable authentication, necessary to guarantee lawful trade and healthy consumption. Alterations or errors in this process can lead to commercial fraud and/or health threats. Consequently, the development of new investigative tools became crucial in ensuring unwanted scenarios. Here we used NGS techniques through targeted metagenomics approach on the V3-V4 region of the 16S rRNA genes to characterize the gill bacterial communities in wild-caught seabream (Sparus aurata) and seabass (Dicentrarchus labrax) within different fisheries areas of the "Costa degli Etruschi'' area in the Tuscan coast. Our challenge involved the possibility of discriminating between the microbiota of both fish species collected from three different fishing sites very close to each other (all within 100 km) in important areas from a commercial and tourist point of view.

Results: Our results showed a significant difference in the assembly of gill bacterial communities in terms of diversity (alpha and beta diversity) of both seabass and seabream in accordance with the three fishing areas. These differences were represented by a unique site -related bacterial signature, more evident in seabream compared to the seabass. Accordingly, the core membership of seabream specimens within the three different sites was minimal compared to the seabass which showed a greater number of sequence variants shared among the different fishing sites. Therefore, the LRT analysis highlighted the possibility of obtaining specific fish bacterial signatures associated with each site; it is noteworthy that specific taxa showed a unique association with the fishing site regardless of the fish species. This study demonstrates the effectiveness of target-metagenomic sequencing of gills in discriminating bacterial signatures of specimens collected from fishing areas located at a limited distance to each other.

Conclusions: This study provides new information relating the structure of the gill microbiota of seabass and seabream in a fishing area with a crucial commercial and tourist interest, namely "Costa degli Etruschi". This study demonstrated that microbiome-based approaches can represent an important tool for validating the seafood origins with a central applicative perspective in the seafood traceability system.

背景:多年来,海产品消费和贸易不断增长,随着其预期的扩大,给海产品行业和政府机构带来了重大挑战。特别是,全球水产品贸易和随之而来的消费与可靠的认证有关,而可靠的认证是保证合法贸易和健康消费的必要条件。这一过程中的改动或错误可能导致商业欺诈和/或健康威胁。因此,开发新的调查工具对于确保不出现意外情况至关重要。在这里,我们通过 16S rRNA 基因 V3-V4 区域的靶向元基因组学方法,使用 NGS 技术描述了托斯卡纳海岸 "Costa degli Etruschi''"地区不同渔业区野生捕捞的鲷鱼(Sparus aurata)和鲈鱼(Dicentrarchus labrax)鳃细菌群落的特征。我们面临的挑战是,从商业和旅游角度来看,这三个重要地区的三个不同渔场距离很近(均在 100 公里以内),如何区分从这三个渔场采集的这两种鱼类的微生物群:结果:我们的研究结果表明,鲈鱼和鲷鱼鳃部细菌群落的多样性(α和β多样性)在三个渔场之间存在明显差异。这些差异表现为与捕捞地点相关的独特细菌特征,与鲈鱼相比,鲷鱼更为明显。因此,与鲈鱼相比,鲷鱼标本在三个不同地点的核心成员数量极少,而鲈鱼则在不同捕鱼地点共享更多的序列变异。因此,LRT 分析强调了获得与每个捕鱼地点相关的特定鱼类细菌特征的可能性;值得注意的是,无论鱼类种类如何,特定分类群都显示出与捕鱼地点的独特关联。这项研究表明,对鳃进行目标-元基因组测序能有效区分从相距有限的渔区采集的标本的细菌特征:本研究提供了有关鲈鱼和鲷鱼鳃微生物群结构的新信息,该地区是一个具有重要商业和旅游价值的渔区,即 "Costa degli Etruschi"。这项研究表明,基于微生物组的方法是验证海产品来源的重要工具,在海产品可追溯系统中具有重要的应用前景。
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引用次数: 0
Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves. 膳食碳水化合物来源对小牛完整肠道的微生物生态系统而非上皮基因表达谱具有不同的刺激作用。
Q1 MICROBIOLOGY Pub Date : 2024-03-13 DOI: 10.1186/s42523-024-00297-5
Thomas Hartinger, Cátia Pacífico, Arife Sener-Aydemir, Gregor Poier, Susanne Kreuzer-Redmer, Georg Terler, Fenja Klevenhusen, Qendrim Zebeli

Background: Recent data indicated similar growth performance of young calves fed solely high-quality hay instead of a starter diet based on starchy ingredients. Yet, providing exclusively such distinct carbohydrate sources during early life might specifically prime the microbiota and gene expression along the gut of young calves, which remains to be explored. We investigated the effects of starter diets differing in carbohydrate composition, that is medium- or high-quality hay and without or with 70% concentrate supplementation (on fresh matter basis), across the gastrointestinal tract (GIT) of weaned Holstein calves (100 ± 4 days of age) using 16 S rRNA gene sequencing and analyses of short-chain fatty acids and host epithelial gene expressions.

Results: The concentrate supplementation drastically decreased microbial diversity throughout the gut, which was also true to a much lesser extent for high-quality hay when compared to medium-quality hay in the foregut. Similarly, the factor concentrate strongly shaped the diet-associated common core microbiota, which was substantially more uniform along the gut with concentrate supplementation. The fermentation profile shifted towards less acetate but more propionate with concentrate supplementation in almost all gut sections, corresponding with higher abundances of starch-utilizing bacteria, while major fibrolytic clusters declined. Noteworthy, the n-butyrate proportion decreased in the rumen and increased in the colon with concentrate, showing an opposite, gut site-dependent effect. Both dietary factors modestly influenced the host epithelial gene expression.

Conclusions: Concentrate supplementation clearly primed the microbial ecosystem on a starch-targeted fermentation with characteristic genera occupying this niche along the entire GIT of calves, whereas the microbial differentiation due to hay quality was less distinct. Overall, changes in the microbial ecosystem were only marginally reflected in the targeted transcriptional profile of the host epithelium.

背景:最近的数据表明,只喂优质干草而不喂以淀粉为基础的开食料的犊牛具有相似的生长性能。然而,在犊牛生命早期专门提供这种不同的碳水化合物来源可能会对犊牛肠道内的微生物群和基因表达产生特殊的刺激作用,这一点仍有待探索。我们利用 16 S rRNA 基因测序以及短链脂肪酸和宿主上皮基因表达分析,研究了不同碳水化合物组成的初生犊牛日粮(即中等或优质干草,不添加或添加 70% 的精料(以新鲜物质为基础))对断奶荷斯坦犊牛(100 ± 4 日龄)胃肠道的影响:结果:补充精料大大降低了整个肠道的微生物多样性,与前肠的中等质量干草相比,优质干草的微生物多样性也大大降低。同样,精料因素对与日粮相关的共同核心微生物群也有很大影响,在补充精料的情况下,肠道内的微生物群更加均匀。在几乎所有的肠道部分,添加精料后发酵产物的乙酸含量减少,而丙酸含量增加,这与淀粉利用细菌的丰度增加相对应,同时主要的纤维分解菌群减少。值得注意的是,随着精料的添加,瘤胃中的正丁酸比例下降,而结肠中的正丁酸比例上升,显示出一种相反的肠道部位依赖效应。两种膳食因素都对宿主上皮基因表达产生了适度影响:结论:补充精料明显使微生物生态系统以淀粉为目标进行发酵,在犊牛的整个消化道中,有特征的菌属占据了这一生态位,而干草质量导致的微生物分化则不那么明显。总体而言,微生物生态系统的变化仅在一定程度上反映在宿主上皮细胞的目标转录谱上。
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引用次数: 0
Interkingdom interactions shape the fungal microbiome of mosquitoes. 王国间的相互作用塑造了蚊子的真菌微生物群。
Q1 MICROBIOLOGY Pub Date : 2024-03-07 DOI: 10.1186/s42523-024-00298-4
Shivanand Hegde, Kamil Khanipov, Emily A Hornett, Pornjarim Nilyanimit, Maria Pimenova, Miguel A Saldaña, Charissa de Bekker, George Golovko, Grant L Hughes

Background: The mosquito microbiome is an important modulator of vector competence and vectoral capacity. Unlike the extensively studied bacterial microbiome, fungal communities in the mosquito microbiome (the mycobiome) remain largely unexplored. To work towards getting an improved understanding of the fungi associated with mosquitoes, we sequenced the mycobiome of three field-collected and laboratory-reared mosquito species (Aedes albopictus, Aedes aegypti, and Culex quinquefasciatus).

Results: Our analysis showed both environment and host species were contributing to the diversity of the fungal microbiome of mosquitoes. When comparing species, Ae. albopictus possessed a higher number of diverse fungal taxa than Cx. quinquefasciatus, while strikingly less than 1% of reads from Ae. aegypti samples were fungal. Fungal reads from Ae. aegypti were < 1% even after inhibiting host amplification using a PNA blocker, indicating that this species lacked a significant fungal microbiome that was amplified using this sequencing approach. Using a mono-association mosquito infection model, we confirmed that mosquito-derived fungal isolates colonize Aedes mosquitoes and support growth and development at comparable rates to their bacterial counterparts. Strikingly, native bacterial taxa isolated from mosquitoes impeded the colonization of symbiotic fungi in Ae. aegypti suggesting interkingdom interactions shape fungal microbiome communities.

Conclusion: Collectively, this study adds to our understanding of the fungal microbiome of different mosquito species, that these fungal microbes support growth and development, and highlights that microbial interactions underpin fungal colonization of these medically relevent species.

背景:蚊子微生物组是病媒能力和病媒传播能力的重要调节器。与被广泛研究的细菌微生物组不同,蚊子微生物组(真菌生物组)中的真菌群落在很大程度上仍未被探索。为了更好地了解与蚊子相关的真菌,我们对三种野外采集和实验室饲养的蚊子(白纹伊蚊、埃及伊蚊和库蚊)的真菌生物群进行了测序:我们的分析表明,环境和宿主物种对蚊子真菌微生物组的多样性都有影响。在物种比较中,白纹伊蚊比五带喙库蚊拥有更多不同的真菌类群,而来自埃及伊蚊样本的真菌读数却不足1%。埃及伊蚊的真菌读数是 结论:总之,这项研究增加了我们对不同蚊子物种真菌微生物组的了解,这些真菌微生物支持了蚊子的生长和发育,并强调了微生物的相互作用是这些具有医学价值的物种真菌定殖的基础。
{"title":"Interkingdom interactions shape the fungal microbiome of mosquitoes.","authors":"Shivanand Hegde, Kamil Khanipov, Emily A Hornett, Pornjarim Nilyanimit, Maria Pimenova, Miguel A Saldaña, Charissa de Bekker, George Golovko, Grant L Hughes","doi":"10.1186/s42523-024-00298-4","DOIUrl":"10.1186/s42523-024-00298-4","url":null,"abstract":"<p><strong>Background: </strong>The mosquito microbiome is an important modulator of vector competence and vectoral capacity. Unlike the extensively studied bacterial microbiome, fungal communities in the mosquito microbiome (the mycobiome) remain largely unexplored. To work towards getting an improved understanding of the fungi associated with mosquitoes, we sequenced the mycobiome of three field-collected and laboratory-reared mosquito species (Aedes albopictus, Aedes aegypti, and Culex quinquefasciatus).</p><p><strong>Results: </strong>Our analysis showed both environment and host species were contributing to the diversity of the fungal microbiome of mosquitoes. When comparing species, Ae. albopictus possessed a higher number of diverse fungal taxa than Cx. quinquefasciatus, while strikingly less than 1% of reads from Ae. aegypti samples were fungal. Fungal reads from Ae. aegypti were < 1% even after inhibiting host amplification using a PNA blocker, indicating that this species lacked a significant fungal microbiome that was amplified using this sequencing approach. Using a mono-association mosquito infection model, we confirmed that mosquito-derived fungal isolates colonize Aedes mosquitoes and support growth and development at comparable rates to their bacterial counterparts. Strikingly, native bacterial taxa isolated from mosquitoes impeded the colonization of symbiotic fungi in Ae. aegypti suggesting interkingdom interactions shape fungal microbiome communities.</p><p><strong>Conclusion: </strong>Collectively, this study adds to our understanding of the fungal microbiome of different mosquito species, that these fungal microbes support growth and development, and highlights that microbial interactions underpin fungal colonization of these medically relevent species.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10921588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061438","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}
引用次数: 0
Removal of leftover feed shapes environmental microbiota and limits houseflies-mediated dispersion of pathogenic bacteria in sow breeding farms. 清除剩余饲料可改变环境微生物群,并限制家蝇介导的病原菌在母猪繁殖场的传播。
Q1 MICROBIOLOGY Pub Date : 2024-03-05 DOI: 10.1186/s42523-024-00296-6
Yunke Li, Yinfeng Chen, Zhaohui Chen, Ying Yang, Zhenlong Wu

Background: Intensive swine breeding industry generates a complex environment where several microbial interactions occur and which constitutes a challenge for biosafety. Ad libitum feeding strategies and low levels of management contribute to residual and wasted feed for lactating sows, which provides a source of nutrients and microbial source for houseflies in warm climates. Due to the absence of the all-in/all-out system, the coexistence of sows of two production stages including gestating and lactating sows in the farrowing barn may have potential negative impacts. In this research, we evaluated the effects of lactating sow leftover on the environmental microbiota of the farrowing barn and the contribution of microbial environments to the gestating sow fecal bacterial structure with a 30-day-long treatment of timely removing lactating residual feed.

Results: Houseflies in the farrowing barn mediate the transmission of microorganisms from lactating sow leftover to multiple regions. Leuconostoc, Weissella, Lactobacillus and Pediococcus from the leftover which can produce exopolysaccharides, are more capable of environmental transmission than pathogenic microorganisms including Staphylococcus and Streptococcus and utilize houseflies to achieve spread in environmental regions of the farrowing barn. Leftover removal treatment blocked the microbial transmission chain mediated by houseflies, downregulated the relative abundance of pathogenic bacteria including Escherichia-Shigella and Streptococcus among houseflies, environmental regions and fecal bacteria of gestating sows in the farrowing barn and effectively attenuate the increment of Weissella and RF39 relative abundance in gestating sow feces due to the presence of lactating sows.

Conclusions: Lactating sow leftover is a non-negligible microbial contributor of environment in farrowing barn whose transmission is mediated by houseflies. A 30-day-long treatment of removing lactating sow residual feed cause significant changes in the microbial structure of multiple environmental regions within the farrowing barn via altering the microbiota carried by houseflies. Meanwhile, lactating sow leftover affect the fecal microbial structure of gestating sows in the same farrowing barn, while removal of lactating sow leftover alleviates the contribution of microbial transmission.

背景:集约化养猪业产生了一个复杂的环境,在这个环境中会发生多种微生物相互作用,这对生物安全构成了挑战。自由采食策略和低水平管理造成哺乳母猪饲料残留和浪费,这为温暖气候条件下的家蝇提供了营养源和微生物源。由于没有全进全出系统,两个生产阶段的母猪(包括妊娠母猪和哺乳母猪)在产房共存可能会产生潜在的负面影响。在这项研究中,我们评估了哺乳母猪剩余饲料对产房环境微生物群的影响,以及微生物环境对妊娠母猪粪便细菌结构的贡献:结果:产仔舍中的家蝇介导了哺乳母猪残余饲料中的微生物向多个区域的传播。剩料中能产生外多糖的白色念珠菌、魏氏菌、乳酸杆菌和乳球菌比葡萄球菌和链球菌等病原微生物的环境传播能力更强,它们利用家蝇实现了在产房环境区域的传播。清除剩菜处理阻断了以家蝇为媒介的微生物传播链,降低了家蝇、环境区域和产房后备母猪粪便细菌中致病菌(包括志贺氏菌和链球菌)的相对丰度,并有效减缓了后备母猪粪便中魏氏菌和RF39相对丰度因哺乳母猪的存在而增加:哺乳母猪粪便是产房环境中不可忽视的微生物贡献者,其传播途径是家蝇。为期 30 天的清除哺乳母猪残余饲料的处理会通过改变家蝇携带的微生物群来显著改变产房内多个环境区域的微生物结构。同时,哺乳母猪的残余饲料会影响同一产房内妊娠母猪的粪便微生物结构,而清除哺乳母猪的残余饲料则会减轻微生物传播的影响。
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引用次数: 0
Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance. 富含酵母甘露聚糖的部分对微生物组的均匀性、与生产力相关的类群和产蛋性能有积极影响。
Q1 MICROBIOLOGY Pub Date : 2024-03-04 DOI: 10.1186/s42523-024-00295-7
Robert J Leigh, Aoife Corrigan, Richard A Murphy, Jules Taylor-Pickard, Colm A Moran, Fiona Walsh

Background: Alternatives to antibiotic as growth promoters in agriculture, such as supplemental prebiotics, are required to maintain healthy and high performing animals without directly contributing to antimicrobial resistance bioburden. While the gut microbiota of broiler hens has been well established and successfully correlated to performance, to our knowledge, a study has yet to be completed on the effect of prebiotic supplementation on correlating the mature laying hen productivity and microbiota. This study focused on establishing the impact of a yeast derived prebiotic, mannan rich fraction (MRF), on the cecal microbiota of late laying hens. This study benefitted from large sample sizes so intra- and intergroup variation effects could be statistically accounted for.

Results: Taxonomic richness was significantly greater at all taxonomic ranks and taxonomic evenness was significantly lower for all taxonomic ranks in MRF-supplemented birds (P < 0.005). Use of principal coordinate analyses and principal component analyses found significant variation between treatment groups. When assessed for compositional uniformity (an indicator of flock health), microbiota in MRF-supplemented birds was more uniform than control birds at the species level. From a food safety and animal welfare perspective, Campylobacter jejuni was significantly lower in abundance in MRF-supplemented birds. In this study, species associated with high weight gain (an anticorrelator of performance in laying hens) were significantly lower in abundance in laying hens while health-correlated butyrate and propionate producing species were significantly greater in abundance in MRF-supplemented birds.

Conclusions: The use of prebiotics may be a key factor in controlling the microbiota balance limiting agri-food chain pathogen persistence and in promoting uniformity. In previous studies, increased α- and β-diversity indices were determinants of pathogen mitigation and performance. MRF-supplemented birds in this study established greater α- and β-diversity indices in post-peak laying hens, greater compositional uniformity across samples, a lower pathogenic bioburden and a greater abundance of correlators of performance.

背景:在农业生产中,需要有替代抗生素的生长促进剂,如补充益生素,以维持健康和高生产性能的动物,同时又不直接造成抗菌素耐药性的生物负担。虽然肉鸡的肠道微生物群已被充分确定并成功地与生产性能相关联,但据我们所知,有关补充益生素对成熟蛋鸡生产率和微生物群相关性的影响的研究尚未完成。本研究的重点是确定酵母提取的益生元--富含甘露聚糖的部分(MRF)对晚产蛋鸡盲肠微生物群的影响。这项研究得益于样本量大,因此组内和组间的变异效应都能在统计学上得到考虑:结果:在添加了 MRF 的鸡只中,所有分类等级的分类丰富度都明显增加,而所有分类等级的分类均匀度都明显降低(P 结论:添加了 MRF 的鸡只中,微生物群的丰富度和均匀度都明显增加,而所有分类等级的分类均匀度都明显降低:益生素的使用可能是控制微生物区系平衡、限制农业食品链病原体持久性和促进均匀性的关键因素。在以前的研究中,α 和 β 多样性指数的增加是病原体缓解和生产性能的决定因素。在本研究中,添加了 MRF 的蛋鸡在产蛋高峰期后的α和β多样性指数更高,各样品的成分均匀性更高,病原体生物负荷更低,生产性能相关因子更丰富。
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引用次数: 0
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Animal microbiome
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