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Insect live larvae as a new nutritional model in duck: effects on gut health. 昆虫活幼虫作为鸭的新营养模型:对肠道健康的影响。
Q1 MICROBIOLOGY Pub Date : 2024-05-29 DOI: 10.1186/s42523-024-00316-5
Elena Colombino, Marta Gariglio, Ilaria Biasato, Ilario Ferrocino, Sara Pozzo, Emma Fragola, Elena Battisti, Stefania Zanet, Ezio Ferroglio, Maria Teresa Capucchio, Achille Schiavone

Background: This study aimed to evaluate the effects of Hermetia illucens (Black soldier fly-BSF) and Tenebrio molitor (Yellow mealworm-YMW) live larvae as a new nutritional model on duck's gut health, considering gut histomorphometry, mucin composition, cytokines transcription levels, and microbiota. A total of 126, 3-days-old, females Muscovy ducks were randomly allotted to three dietary treatments (6 replicates/treatment, 7 birds/pen): (i) C: basal diet; (ii) BSF: C + BSF live larvae; (iii) YMW: C + YMW live larvae. BSF and YMW live larvae were administered on top of the basal diet, based on the 5% of the expected daily feed intake. The live weight, average daily gain, average daily feed intake and feed conversion ratio were evaluated for the whole experimental period. On day 52, 12 ducks/treatment (2 birds/replicate) were slaughtered and samples of duodenum, jejunum, ileum, spleen, liver, thymus and bursa of Fabricius were collected for histomorphometry. Mucin composition was evaluated in the small intestine through histochemical staining while jejunal MUC-2 and cytokines transcription levels were evaluated by rt-qPCR. Cecal microbiota was also analyzed by means of 16 S rRNA gene sequencing.

Results: Birds' growth performance and histomorphometry were not influenced by diet, with a proximo-distal decreasing gradient from duodenum to ileum (p < 0.001), respecting the physiological gut development. Mucin staining intensity and MUC-2 gene expression did not vary among dietary treatments, even though mucin intensity increased from duodenum to ileum, according to normal gut mucus physiology (p < 0.001). Regarding local immune response, IL-6 was higher in YMW group when compared to the other groups (p = 0.009). Insect live larvae did not affect cecal microbiota diversity, but BSF and YMW groups showed a higher presence of Helicobacter, Elusimicrobium, and Succinatimonas and a lower abundance of Coriobacteriaceae and Phascolarctobacterium compared to C birds (p < 0.05).

Conclusions: The use of BSF and YMW live larvae as new nutritional model did not impair gut development and mucin composition of Muscovy ducks, but slightly improved the intestinal immune status and the microbiota composition by enhancing regulatory cytokine IL-6 and by increasing minor Operational Taxonomic Units (OTUs) involved in short-chain fatty acids production.

背景:本研究旨在评估作为一种新的营养模型的Hermetia illucens(黑兵蝇-BSF)和Tenebrio molitor(黄粉虫-YMW)活幼虫对鸭肠道健康的影响,包括肠道组织形态测量、粘蛋白组成、细胞因子转录水平和微生物群。将 126 只 3 日龄的雌性莫斯科鸭随机分配到三种日粮处理中(每种处理 6 个重复,每栏 7 只):(i) C:基础日粮;(ii) BSF:C + BSF 活幼虫;(iii) YMW:C + YMW 活幼虫。BSF 和 YMW 活幼虫是在基础日粮基础上添加的,以预期日饲料摄入量的 5%为基础。对整个实验期间的活重、平均日增重、平均日采食量和饲料转化率进行了评估。第 52 天,宰杀每个处理的 12 只鸭子(2 只/重复),收集十二指肠、空肠、回肠、脾脏、肝脏、胸腺和法氏囊样本,进行组织形态测定。通过组织化学染色评估小肠粘蛋白的组成,同时通过 rt-qPCR 评估空肠 MUC-2 和细胞因子的转录水平。还通过 16 S rRNA 基因测序分析了盲肠微生物群:结果:鸟类的生长性能和组织形态学不受日粮的影响,从十二指肠到回肠呈近端-远端递减梯度(p 结论):使用 BSF 和 YMW 活幼虫作为新的营养模型不会影响高加索鸭的肠道发育和粘蛋白组成,但通过提高调节细胞因子 IL-6 和增加参与短链脂肪酸生产的次要操作分类单元 (OTU),略微改善了肠道免疫状态和微生物群组成。
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引用次数: 0
Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis. 整合子宫微生物组和代谢组,加深对患子宫炎奶牛子宫环境的了解。
Q1 MICROBIOLOGY Pub Date : 2024-05-27 DOI: 10.1186/s42523-024-00314-7
S Casaro, J G Prim, T D Gonzalez, F Cunha, R S Bisinotto, R C Chebel, J E P Santos, C D Nelson, S J Jeon, R C Bicalho, J P Driver, Klibs N Galvão

Background: Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days postpartum, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine microbiome and metabolome data to advance the understanding of the uterine environment in dairy cows that develop metritis. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine microbiome and metabolome were evaluated individually, and then integrated using network analyses.

Results: The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows that did and did not develop metritis. Omics integration was performed between 6 significant bacteria genera and 153 significant metabolites on the day of metritis diagnosis. Integration was not performed at calving because there were no significant differences in the uterine microbiome. A total of 3 bacteria genera (i.e. Fusobacterium, Porphyromonas, and Bacteroides) were strongly correlated with 49 metabolites on the day of metritis diagnosis. Seven of the significant metabolites at calving were among the 49 metabolites strongly correlated with opportunistic pathogenic bacteria on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, opportunistic pathogenic bacteria overgrowth, tissue damage and inflammation, immune evasion, and immune dysregulation.

Conclusions: The data integration presented herein helps advance the understanding of the uterine environment in dairy cows with metritis. The identified metabolites may provide a competitive advantage to the main uterine pathogens Fusobacterium, Porphyromonas and Bacteroides, and may be promising targets for future interventions aiming to reduce opportunistic pathogenic bacteria growth in the uterus.

背景:子宫炎是一种常见的子宫疾病,会影响奶牛的福利、繁殖力和存活率。从产犊到产后 2 天,患子宫炎的奶牛和保持健康的奶牛的子宫微生物群并无不同,产后 2 天后,子宫微生物群出现菌群失调,其特征是转向机会性病原体,如镰刀菌属和类杆菌属。这些机会性病原体是否会增殖并超越子宫共生菌,可能取决于子宫中存在的基质类型。本研究的目的是整合子宫微生物组和代谢组数据,以加深对发生子宫炎的奶牛子宫环境的了解。荷斯坦奶牛(104 头)在产仔时和诊断出元胞炎时采集了子宫液。根据产犊后天数,将患有元气大伤的奶牛(n = 52)与未患元气大伤的奶牛(n = 52)配对。首先对子宫微生物组和代谢组进行单独评估,然后利用网络分析法对其进行整合:结果:子宫微生物组在产犊时没有差异,但在确诊元气大伤当天,有元气大伤的奶牛和没有元气大伤的奶牛的子宫微生物组存在差异。子宫代谢组在产犊时和确诊元气淋巴结炎当天在患元气淋巴结炎和未患元气淋巴结炎的奶牛之间存在差异。在元气大伤确诊当天,对 6 个重要细菌属和 153 个重要代谢物进行了 Omics 整合。由于子宫微生物组没有显著差异,因此没有在产犊时进行整合。共有 3 个菌属(即 Fusobacterium、Porphyromonas 和 Bacteroides)与元气大伤诊断当天的 49 个代谢物密切相关。在产犊时的 49 种代谢物中,有 7 种代谢物与元气大伤确诊当天的机会致病菌密切相关。主要代谢物与减少共生细菌形成生物膜、机会致病菌过度生长、组织损伤和炎症、免疫逃避和免疫失调有关:本文提供的数据整合有助于加深对患子宫炎奶牛子宫环境的了解。鉴定出的代谢物可能为子宫主要病原体镰刀菌、卟啉单胞菌和巴氏杆菌提供了竞争优势,并可能成为未来旨在减少子宫内机会性致病菌生长的干预目标。
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引用次数: 0
Microbial dynamics and vertical transmission of Escherichia coli across consecutive life stages of the black soldier fly (Hermetia illucens). 大肠埃希氏菌在黑兵蝇(Hermetia illucens)连续生命阶段中的微生物动态和垂直传播。
Q1 MICROBIOLOGY Pub Date : 2024-05-26 DOI: 10.1186/s42523-024-00317-4
Noor Van Looveren, Freek IJdema, Niels van der Heijden, Mik Van Der Borght, Dries Vandeweyer

Background: The black soldier fly (BSF, Hermetia illucens L.) is one of the most promising insects for bioconversion of organic waste, which often carry a high microbial load with potential foodborne pathogens. Although horizontal transmission (from rearing substrate to larvae) has been extensively studied, less is known about vertical transmission of microorganisms, and particularly of foodborne pathogens, across different BSF life stages.

Results: This study investigated the microbial dynamics and vertical transmission of Escherichia coli across different life stages (larvae, prepupae, pupae and adults) of one BSF life cycle and its associated substrate (chicken feed) and frass, based on a combination of general microbial counts (based on culture-dependent techniques) and the bacterial community composition (based on 16S rRNA gene sequencing). Multiple interactions between the microbiota of the substrate, frass and BSF larvae were affirmed. The larvae showed relative consistency among both the microbial counts and bacterial community composition. Diversification of the bacterial communities started during the pupal stage, while most notable changes of the microbial counts and bacterial community compositions occurred during metamorphosis to adults. Furthermore, vertical transmission of E. coli was investigated after substrate inoculation with approximately 7.0 log cfu/g of kanamycin-resistant E. coli, and monitoring E. coli counts from larval to adult stage. Although the frass still contained substantial levels of E. coli (> 4.5 log cfu/g) and E. coli was taken up by the larvae, limited vertical transmission of E. coli was observed with a decreasing trend until the prepupal stage. E. coli counts were below the detection limit (1.0 log cfu/g) for all BSF samples from the end of the pupal stage and the adult stage. Additionally, substrate inoculation of E. coli did not have a substantial impact on the bacterial community composition of the substrate, frass or different BSF life stages.

Conclusions: The fluctuating microbial counts and bacterial community composition underscored the dynamic character of the microbiota of BSF life stages. Additionally, vertical transmission throughout one BSF life cycle was not observed for E. coli. Hence, these findings paved the way for future case studies on vertical transmission of foodborne pathogens across consecutive BSF life stages or other insect species.

背景:黑兵蝇(BSF,Hermetia illucens L.)是最有希望对有机废物进行生物转化的昆虫之一,而有机废物中往往含有大量微生物和潜在的食源性病原体。虽然对横向传播(从饲养基质到幼虫)进行了广泛研究,但对微生物,特别是食源性病原体在 BSF 不同生命阶段的纵向传播了解较少:本研究根据一般微生物计数(基于依赖培养的技术)和细菌群落组成(基于 16S rRNA 基因测序),调查了大肠埃希氏菌在一个 BSF 生命周期的不同生命阶段(幼虫、蛹、蛹和成虫)及其相关基质(鸡饲料)和粪便中的微生物动态和垂直传播。基质、粪便和 BSF 幼虫的微生物群落之间存在多种相互作用。幼虫在微生物数量和细菌群落组成方面表现出相对的一致性。细菌群落的多样化始于蛹期,而微生物数量和细菌群落组成的最显著变化则发生在成虫蜕变期。此外,在基质中接种约 7.0 log cfu/g 的耐卡那霉素大肠杆菌,并监测从幼虫到成虫阶段的大肠杆菌数量后,研究了大肠杆菌的垂直传播。尽管虫粪中仍含有大量大肠杆菌(> 4.5 log cfu/g),而且幼虫也吸收了大肠杆菌,但观察到大肠杆菌的垂直传播有限,且呈下降趋势,直至成虫期。在蛹末期和成虫期的所有 BSF 样品中,大肠杆菌计数均低于检测限(1.0 log cfu/g)。此外,在基质中接种大肠杆菌对基质、虫粪或 BSF 不同生命阶段的细菌群落组成没有实质性影响:微生物数量和细菌群落组成的波动凸显了 BSF 生命阶段微生物群落的动态特征。此外,在 BSF 的一个生命周期中没有观察到大肠杆菌的垂直传播。因此,这些发现为今后开展有关食源性病原体在连续的 BSF 生命阶段或其他昆虫物种之间垂直传播的案例研究铺平了道路。
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引用次数: 0
Early-life factors shaping the gut microbiota of Common buzzard nestlings. 影响鵟雏鸟肠道微生物群的早期因素
Q1 MICROBIOLOGY Pub Date : 2024-05-14 DOI: 10.1186/s42523-024-00313-8
Hugo Pereira, Nayden Chakarov, Joseph I Hoffman, Tony Rinaud, Meinolf Ottensmann, Kai-Philipp Gladow, Busche Tobias, Barbara A Caspers, Öncü Maraci, Oliver Krüger

Background: Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors.

Results: We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition.

Conclusion: Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.

背景:探索生命早期阶段肠道微生物群定植的动态对于了解微生物对宿主发育和健康的潜在影响非常重要。来自模式生物的证据表明,在生命早期的一个关键阶段,肠道微生物群的变化可能会导致免疫失调和宿主状况下降。然而,我们对长寿脊椎动物肠道微生物群定植的了解仍然有限,尤其是在早期发育阶段。因此,我们利用普通鵟雏鸟(Buteo buteo)的野生种群来研究生命早期肠道微生物群定植、环境和宿主因素之间的联系:我们使用 16S 和 28S rRNA 基因对细菌和真核微生物群进行了定位。我们采用纵向设计对早期发育阶段的个体进行了采样。我们的数据显示,年龄对微生物的多样性和组成有很大影响。巢穴环境是预测微生物群组成的一个重要因素,尤其是真核生物群落在宿主占据的栖息地之间存在差异。雏鸟的状况和血液寄生虫白细胞虫的感染可预测微生物群落的组成:我们的研究结果强调了研究微生物群动态以捕捉本体发生变化的重要性。研究结果强调了微生物群落在反映宿主健康方面的作用,以及巢穴环境对发育中的雏鸟微生物群落的重要性。总之,这项研究有助于理解微生物群落、宿主因素和环境变量之间复杂的相互作用,并揭示了生命早期阶段肠道微生物定植的生态过程。
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引用次数: 0
A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts. 野外的滋味:补充饲喂赤鹿(Cervus elaphus)可增加个体细菌微生物群的多样性,但会降低重要肠道共生菌的丰度。
Q1 MICROBIOLOGY Pub Date : 2024-05-14 DOI: 10.1186/s42523-024-00315-6
Luis Víquez-R, Maik Henrich, Vanessa Riegel, Marvin Bader, Kerstin Wilhelm, Marco Heurich, Simone Sommer

The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.

肠道微生物群对动物的健康和福祉起着至关重要的作用。对于依赖细菌群落消化食物的反刍动物来说,这一点尤为重要。在这项研究中,我们调查了管理条件和补饲对德国巴伐利亚森林国家公园中的马鹿(Cervus elaphus)肠道细菌微生物群的影响。我们从自由放养的鹿、冬季圈养的鹿和永久性圈养的鹿身上采集了粪便样本。对样本进行了 16 S rRNA 基因高通量测序分析。结果表明,不同管理组内部和之间的肠道细菌微生物群在多样性、丰度和异质性方面存在差异。与圈养的鹿相比,自由放养的鹿表现出较低的α多样性,这可能是因为圈养的鹿有食物补充。自由生活的个体也表现出最高的β多样性,这表明觅食地和植物物种选择的差异性更大。此外,自由活动的鹿体内潜在致病细菌类群的丰度最低,这表明它们的肠道微生物组更健康。冬季圈养的鹿在围栏中度过一段时间后,表现出介于自由放养鹿和全年圈养鹿之间的特征。这些研究结果表明,冬季圈养管理策略,包括用加工过的植物和作物进行补充饲喂,对红鹿肠道微生物组的组成有重大影响。总之,这项研究为了解管理条件,尤其是冬季圈养措施对马鹿肠道微生物组的影响提供了重要见解。了解这些影响对于评估管理策略对健康的潜在影响至关重要,并凸显了微生物群调查作为健康标志物的价值。
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引用次数: 0
Volatiles of symbiotic bacterial origin explain ectoparasitism and fledging success of hoopoes. 源于共生细菌的挥发性物质解释了胡蜂的外寄生性和羽化成功率。
Q1 MICROBIOLOGY Pub Date : 2024-05-10 DOI: 10.1186/s42523-024-00312-9
Mónica Mazorra-Alonso, Juan Manuel Peralta-Sánchez, Manuel Martín-Vivaldi, Manuel Martínez-Bueno, Rafael Núñez Gómez, Juan José Soler

Background: Some parasites use olfactory cues to detect their hosts and, since bacterial symbionts are partially responsible for animal odours, they could influence host parasitism. By autoclaving nest materials of hoopoe (Upupa epops) nests before reproduction started, we explored the hypothetical links between host-associated bacteria, volatiles and parasitism. During the nestling stage, we (i) estimated the level of ectoparasitism by chewing lice (Suborder Mallophaga) in adult hoopoe females and by Carnus haemapterus flies in nestlings, and (ii) characterized microbial communities and volatile profiles of nest environments (nest material and nest cavity, respectively) and uropygial secretions.

Results: Experimental nests had less diverse bacterial communities and more diverse volatile profiles than control nests, while occupants experienced lower intensity of parasitism in experimental than in control nests. The experiment also affected beta diversity of the microbial communities of nest material and of the volatiles of the nestling uropygial secretions. Moreover, microbial communities of uropygial secretions and of nest materials covaried with their volatile profiles, while the volatile profile of the bird secretions explained nest volatile profile. Finally, a subset of the volatiles and bacteria detected in the nest material and uropygial secretions were associated with the ectoparasitism intensity of both adult females and nestlings, and with fledging success.

Conclusions: These results show that a component of animal odours is linked with the microbial communities of the host and its reproductive environment, and emphasize that the associations between bacteria, ectoparasitism and reproductive success are partially mediated by volatiles of bacterial origin. Future work should focus on mechanisms underlying the detected patterns.

背景:一些寄生虫利用嗅觉线索来探测宿主,由于细菌共生体是动物气味的部分来源,它们可能会影响宿主的寄生性。通过在繁殖开始前对鵖(Upupa epops)巢穴材料进行高压灭菌,我们探索了宿主相关细菌、挥发性物质和寄生之间的假设联系。在雏鸟阶段,我们(i)估计了成年雌环斑鸠体内咀嚼虱(Mallophaga亚目)和雏鸟体内Carnus haemapterus苍蝇的体外寄生水平,(ii)描述了巢环境(分别是巢材料和巢腔)和尿囊分泌物的微生物群落和挥发性特征:结果:与对照巢相比,实验巢中细菌群落的多样性较低,挥发性特征的多样性较高。实验还影响了巢材料微生物群落和雏鸟尿道分泌物挥发物的贝塔多样性。此外,尿道分泌物和鸟巢材料的微生物群落与它们的挥发性特征相关,而鸟类分泌物的挥发性特征则解释了鸟巢的挥发性特征。最后,在鸟巢材料和尿囊分泌物中检测到的部分挥发性物质和细菌与成年雌鸟和雏鸟的体外寄生强度以及羽化成功率有关:这些结果表明,动物气味的一个组成部分与宿主及其繁殖环境的微生物群落有关,并强调细菌、外寄生和繁殖成功率之间的联系部分是由细菌挥发物介导的。今后的工作应侧重于研究所发现模式的内在机制。
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引用次数: 0
Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health. 探索家禽呼吸道微生物群的复杂性:定植、组成和对健康的影响。
Q1 MICROBIOLOGY Pub Date : 2024-05-06 DOI: 10.1186/s42523-024-00308-5
Samson Oladokun, Shayan Sharif

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

准确了解家禽呼吸道微生物群的生态学和复杂性,对于阐明呼吸道中共生或致病微生物的作用及其与家禽健康或疾病结果的关系至关重要。本综述深入探讨了家禽呼吸道微生物群的复杂方面,重点关注其定植模式、组成以及对家禽健康的影响。首先,概述了当前有关家禽呼吸道微生物群组成的最新知识,以及影响群落结构和多样性动态的因素。此外,还探讨了家禽呼吸道微生物群在影响家禽的经济相关呼吸道病理学中的重要作用。此外,还探讨了在研究家禽呼吸道微生物群时遇到的挑战,包括微生物群落的动态性质、特定场所的变化、标准化方案的需求、适当的测序技术以及与采样方法相关的局限性。此外,新出现的证据表明家禽肠道和呼吸道微生物群之间存在双向交流,其中一个微生物群的紊乱会影响另一个微生物群。了解这种错综复杂的交叉对话有可能为增强家禽健康和疾病控制提供有价值的见解。显而易见,全面了解家禽呼吸道微生物群的多方面作用(如本综述所述)对于优化家禽健康管理和改善家禽生产的整体结果至关重要。
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引用次数: 0
Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments. 使用常用断奶后腹泻疗法治疗猪的肠道微生物组和抗性组特征。
Q1 MICROBIOLOGY Pub Date : 2024-05-03 DOI: 10.1186/s42523-024-00307-6
Judith Guitart-Matas, Maria Ballester, Lorenzo Fraile, Laila Darwich, Noemí Giler-Baquerizo, Joaquim Tarres, Sergio López-Soria, Yuliaxis Ramayo-Caldas, Lourdes Migura-Garcia

Background: The global burden of antimicrobial resistance demands additional measures to ensure the sustainable and conscious use of antimicrobials. For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. Among them, post-weaning diarrhea causes vast economic losses, as it severely compromises piglets' health and growth performance. In this study, 210 piglets were transferred from a farm with recurrent cases of post-weaning diarrhea to an experimental farm and divided into six different treatment groups to determine the effect of the different treatments on the growth performance and survival, the microbiome, and the resistome in a cross-sectional and longitudinal study. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, and gentamicin, an oral commercial vaccine, a control with water acidification, and an untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. A total of 280 fecal samples from pigs at four different sampling times were selected for metagenomics: before weaning-treatment at the farm of origin, and three days, two weeks, and four weeks post-treatment.

Results: The control group with water acidification showed a reduced death risk in the survival analyses and non-significant differences in average daily weight gain in comparison to the antibiotic-treated groups. However, the growth-promoting effect among antibiotic-treated groups was demonstrated when comparing against the untreated control group at the experimental farm. After four weeks of treatment, diversity indexes revealed significantly decreased diversity for the untreated control and the group that remained at the farm of origin treated with amoxicillin. For this last group, impaired microbial diversity could be related to the continuous amoxicillin treatment carried out at the farm. Analysis of the resistome showed that both gentamicin and amoxicillin treatments significantly contributed to the emergence of resistance, while trimethoprim/sulphonamide and colistin did not, suggesting that different treatments contribute differently to the emergence of resistance.

Conclusions: Overall, this shotgun longitudinal metagenomics analysis demonstrates that non-antibiotic alternatives, such as water acidification, can contribute to reducing the emergence of antimicrobial resistance without compromising pig growth performance and gut microbiome.

背景:抗菌素耐药性给全球造成的负担要求采取更多措施,以确保可持续和有意识地使用抗菌素。对于养猪业来说,断奶后时期至关重要,多年来,抗菌药物一直是控制和治疗断奶后相关感染的最有效策略。其中,断奶后腹泻严重影响仔猪的健康和生长性能,造成巨大的经济损失。本研究将 210 头仔猪从一个断奶后腹泻反复发作的猪场转移到一个实验猪场,并将其分为六个不同的治疗组,通过横向和纵向研究确定不同治疗对仔猪生长性能和存活率、微生物组和抗药性组的影响。不同的处理包括抗菌药物三甲氧苄青霉素/磺胺甲噁唑、可乐定和庆大霉素、口服商业疫苗、水质酸化对照组和未处理对照组。在实施阿莫西林常规治疗后,还有一组留在原产地农场。共选取了 280 份猪粪样本,在四个不同的采样时间进行了元基因组学分析:在原产地猪场进行断奶处理前、处理后三天、两周和四周:结果:与抗生素处理组相比,水酸化对照组在存活分析中的死亡风险降低,平均日增重差异不显著。然而,与实验农场未处理的对照组相比,抗生素处理组具有促进生长的效果。治疗四周后,多样性指数显示,未经治疗的对照组和留在原产地农场接受阿莫西林治疗的组的多样性明显下降。最后一组微生物多样性受损可能与农场持续使用阿莫西林治疗有关。耐药性组的分析表明,庆大霉素和阿莫西林的处理对耐药性的产生有显著的促进作用,而三甲氧苄青霉素/磺胺和可乐定则没有,这表明不同的处理对耐药性的产生有不同的作用:总之,这项猎枪纵向元基因组学分析表明,水酸化等非抗生素替代品有助于减少抗菌素耐药性的产生,而不会影响猪的生长性能和肠道微生物组。
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引用次数: 0
Critical complex network structures in animal gastrointestinal tract microbiomes. 动物胃肠道微生物群的关键复杂网络结构。
Q1 MICROBIOLOGY Pub Date : 2024-05-03 DOI: 10.1186/s42523-024-00291-x
Zhanshan Sam Ma, Peng Shi

Background: Living things from microbes to their hosts (plants, animals and humans) interact with each other, and their relationships may be described with complex network models. The present study focuses on the critical network structures, specifically the core/periphery nodes and backbones (paths of high-salience skeletons) in animal gastrointestinal microbiomes (AGMs) networks. The core/periphery network (CPN) mirrors nearly ubiquitous nestedness in ecological communities, particularly dividing the network as densely interconnected core-species and periphery-species that only sparsely linked to the core. Complementarily, the high-salience skeleton network (HSN) mirrors the pervasive asymmetrical species interactions (strictly microbial species correlations), particularly forming heterogenous pathways in AGM networks with both "backbones" and "rural roads" (regular or weak links). While the cores and backbones can act as critical functional structures, the periphery nodes and weak links may stabilize network functionalities through redundancy.

Results: Here, we build and analyze 36 pairs of CPN/HSN for the AGMs based on 4903 gastrointestinal-microbiome samples containing 473,359 microbial species collected from 318 animal species covering all vertebrate and four major invertebrate classes. The network analyses were performed at host species, order, class, phylum, kingdom scales and diet types with selected and comparative taxon pairs. Besides diet types, the influence of host phylogeny, measured with phylogenetic (evolutionary) timeline or "age", were integrated into the analyses. For example, it was found that the evolutionary trends of three primary microbial phyla (Bacteroidetes/Firmicutes/Proteobacteria) and their pairwise abundance-ratios in animals do not mirror the patterns in modern humans phylogenetically, although they are consistent in terms of diet types.

Conclusions: Overall, the critical network structures of AGMs are qualitatively and structurally similar to those of the human gut microbiomes. Nevertheless, it appears that the critical composition (the three phyla of Bacteroidetes, Firmicutes, and Proteobacteria) in human gut microbiomes has broken the evolutionary trend from animals to humans, possibly attributable to the Anthropocene epoch and reflecting the far-reaching influences of agriculture and industrial revolution on the human gut microbiomes. The influences may have led to the deviations between modern humans and our hunter-gather ancestors and animals.

背景:从微生物到它们的宿主(植物、动物和人类),各种生物相互影响,它们之间的关系可以用复杂的网络模型来描述。本研究的重点是关键网络结构,特别是动物胃肠道微生物组(AGMs)网络中的核心/外围节点和骨干(高效应骨架路径)。核心/外围网络(CPN)反映了生态群落中几乎无处不在的嵌套性,特别是将网络划分为相互联系紧密的核心物种和仅与核心物种有稀疏联系的外围物种。与之互补的是,高体验骨架网络(HSN)反映了普遍存在的不对称物种相互作用(严格意义上的微生物物种相关性),特别是在 AGM 网络中形成了具有 "骨干 "和 "乡村道路"(常规或弱链接)的异质路径。核心和骨干可作为关键的功能结构,而外围节点和薄弱环节则可通过冗余稳定网络功能:在此,我们根据从 318 种动物(涵盖所有脊椎动物和四大无脊椎动物)收集的 4903 份胃肠道微生物组样本(包含 473 359 种微生物),为 AGMs 构建并分析了 36 对 CPN/HSN。网络分析是在宿主物种、纲、目、门、界和饮食类型的范围内,通过选定和比较类群对进行的。除了食性类型外,分析中还考虑了宿主系统发育的影响,用系统发育(进化)时间表或 "年龄 "来衡量。例如,研究发现,动物体内三个主要微生物门(类杆菌属/固缩菌属/蛋白细菌属)的进化趋势及其成对丰度比并不反映现代人类的系统发育模式,尽管它们在饮食类型方面是一致的:总体而言,AGMs 的关键网络结构在质量和结构上与人类肠道微生物组相似。尽管如此,人类肠道微生物组的关键组成(类杆菌、真菌和变形菌三个门)似乎打破了从动物到人类的进化趋势,这可能归因于人类纪,反映了农业和工业革命对人类肠道微生物组的深远影响。这些影响可能导致了现代人类与狩猎采集祖先和动物之间的偏差。
{"title":"Critical complex network structures in animal gastrointestinal tract microbiomes.","authors":"Zhanshan Sam Ma, Peng Shi","doi":"10.1186/s42523-024-00291-x","DOIUrl":"https://doi.org/10.1186/s42523-024-00291-x","url":null,"abstract":"<p><strong>Background: </strong>Living things from microbes to their hosts (plants, animals and humans) interact with each other, and their relationships may be described with complex network models. The present study focuses on the critical network structures, specifically the core/periphery nodes and backbones (paths of high-salience skeletons) in animal gastrointestinal microbiomes (AGMs) networks. The core/periphery network (CPN) mirrors nearly ubiquitous nestedness in ecological communities, particularly dividing the network as densely interconnected core-species and periphery-species that only sparsely linked to the core. Complementarily, the high-salience skeleton network (HSN) mirrors the pervasive asymmetrical species interactions (strictly microbial species correlations), particularly forming heterogenous pathways in AGM networks with both \"backbones\" and \"rural roads\" (regular or weak links). While the cores and backbones can act as critical functional structures, the periphery nodes and weak links may stabilize network functionalities through redundancy.</p><p><strong>Results: </strong>Here, we build and analyze 36 pairs of CPN/HSN for the AGMs based on 4903 gastrointestinal-microbiome samples containing 473,359 microbial species collected from 318 animal species covering all vertebrate and four major invertebrate classes. The network analyses were performed at host species, order, class, phylum, kingdom scales and diet types with selected and comparative taxon pairs. Besides diet types, the influence of host phylogeny, measured with phylogenetic (evolutionary) timeline or \"age\", were integrated into the analyses. For example, it was found that the evolutionary trends of three primary microbial phyla (Bacteroidetes/Firmicutes/Proteobacteria) and their pairwise abundance-ratios in animals do not mirror the patterns in modern humans phylogenetically, although they are consistent in terms of diet types.</p><p><strong>Conclusions: </strong>Overall, the critical network structures of AGMs are qualitatively and structurally similar to those of the human gut microbiomes. Nevertheless, it appears that the critical composition (the three phyla of Bacteroidetes, Firmicutes, and Proteobacteria) in human gut microbiomes has broken the evolutionary trend from animals to humans, possibly attributable to the Anthropocene epoch and reflecting the far-reaching influences of agriculture and industrial revolution on the human gut microbiomes. The influences may have led to the deviations between modern humans and our hunter-gather ancestors and animals.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140872229","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
Correction: Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance. 更正: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 : 2024-05-02 DOI: 10.1186/s42523-024-00310-x
Robert J Leigh, Aoife Corrigan, Richard A Murphy, Jules Taylor-Pickard, Colm A Moran, Fiona Walsh
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引用次数: 0
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Animal microbiome
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