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Gastrointestinal microbiota and metabolites responses to dietary cereal grains in an adult pig model 成年猪模型的胃肠道微生物群和代谢物对日粮谷物的反应
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1442077
Ganyi Feng, Menglong Deng, Rui Li, Gaifeng Hou, Qing Ouyang, Xianji Jiang, Xiaojie Liu, Hui Tang, Fengming Chen, Shihua Pu, Dan Wan, Yulong Yin
Corn (C), wheat (W), and paddy rice (PR) are important energy sources and are commonly used in feed production for swine. This study mainly focuses on the variation and regularities of microbiota and metabolites in the gastrointestinal tract (GIT) of pigs in response to C, W, and PR. A total of 18 pigs were allotted into three dietary groups with six replicated pigs and received diets containing C, W, or PR as the sole energy source, respectively. The results showed that digestive parts significantly affected the diversity of microbial communities. Cereal grain sources significantly influenced the β-diversity of microbial communities in the colon and rectum. Campylobacterota and Proteobacteria are mainly distributed in the duodenum, Lactobacillus in the jejunum, and Bacteroidota in the colon and rectum. The W diet increased the Bacteroidota, Spirochaetota, and Prevotellaceae_NK3B31_group abundances and showed the highest concentrations of all short-chain fatty acids (SCFAs) in the hindgut. Fibrobacterota, Bacteroidota, Spirochaetota, Prevotellaceae_NK3B31_group, Prevotella, and Treponema in the colon or rectum were positively correlated with acetate, propionate, butyrate, and total SCFAs. These findings suggested that aerobic bacteria and facultative anaerobes in the foregut will gradually be replaced by anaerobes in the hindgut. The W diet had the best fermentability and was beneficial to the colonization of microbial communities that mainly used carbohydrates. The hindgut flora of the PR diet group may be more balanced with fewer potential pathogenic bacteria. Many microbial communities have been identified to contribute positively to the SCFA production of the hindgut. Collectively, our study revealed the spatial variation regularities of GIT microbial communities in an adult pig model and provided new insights into GIT microbiota and responses of metabolites to cereal grain diets.
玉米(C)、小麦(W)和稻谷(PR)是重要的能量来源,常用于猪饲料生产。本研究主要关注猪胃肠道(GIT)微生物群和代谢物对玉米、小麦和稻谷的响应变化和规律性。研究人员将 18 头猪分成三个日粮组,每组 6 头猪,分别以 C、W 或 PR 作为唯一的能量来源。结果表明,消化部位对微生物群落的多样性有显著影响。谷物来源对结肠和直肠微生物群落的β-多样性有明显影响。弯曲杆菌和变形杆菌主要分布在十二指肠,乳酸杆菌分布在空肠,类杆菌则分布在结肠和直肠。W 日粮增加了类杆菌、螺旋藻和前螺旋藻_NK3B31_群的丰度,并显示后肠中所有短链脂肪酸(SCFAs)的浓度最高。结肠或直肠中的纤维菌群、类杆菌群、螺壳菌群、前驱菌_NK3B31_组、前驱菌和颤形菌与乙酸盐、丙酸盐、丁酸盐和总 SCFAs 呈正相关。这些发现表明,前肠的需氧菌和兼性厌氧菌将逐渐被后肠的厌氧菌所取代。W 日粮的发酵性最好,有利于主要利用碳水化合物的微生物群落的定植。PR 日粮组的后肠菌群可能更平衡,潜在的致病菌更少。已发现许多微生物群落对后肠SCFA的产生有积极作用。总之,我们的研究揭示了成年猪模型中胃食道微生物群落的空间变化规律,并为胃食道微生物群落和代谢物对谷物日粮的反应提供了新的见解。
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引用次数: 0
Unlocking the potential of Kluyveromyces marxianus in the definition of aroma composition of cheeses 发掘马氏克鲁维氏菌在确定奶酪香气成分方面的潜力
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1464953
Giorgia Perpetuini, Alessio Pio Rossetti, Arianna Rapagnetta, Rosanna Tofalo
IntroductionThe cheese microbiota is very complex and is made up of technologically-relevant, spoilage, opportunistic and pathogenic microorganisms. Among them lactic acid bacteria and yeasts are the main ones. One of the most interesting dairy yeasts is Kluyveromyces marxianus because of its technological properties including the ability to produce aroma compounds.MethodsThis study investigated the contribution of Kluyveromyces marxianus to the gross composition and aroma profile of cow cheeses. Experimental cheeses were prepared by inoculating a co-culture of K. marxianus FM09 and a commercial strain of Lacticaseibacillus casei and compared with cheeses obtained with only L. casei. The gross composition was determined by a FoodScan™ 2 Dairy Analyser, and free amino acids were evaluated at 507 nm after reaction with Cd-ninhydrin. The volatile organic compounds were extracted by head-space solid phase micro-extraction and analyzed by gas chromatography–mass spectrometry coupled with odor activity values. qRT-PCR was applied to determine the expression of genes involved in esters synthesis and degradation.ResultsThe inoculation of K. marxianus induced an increase of pH and a reduction of protein content of cheeses, in agreement with the stronger proteolysis detected in these cheeses. K. marxianus influenced the content of aroma compounds both quantitatively and qualitatively. In particular, an increase of higher alcohols, esters and organic acids was observed. Moreover, 12 compounds were detected only in cheeses obtained with the co-culture. These differences were in agreement with the odor activity values (OAV). In fact, only 11 compounds showed OAV &gt; 1 in cheeses obtained with the commercial strain, and 24 in those obtained with the co-culture. The qPCR analysis revealed an over expression of ATF1, EAT1, and IAH1 genes.ConclusionKluyveromyces marxianus could act as an important auxiliary starter for cheese production through the development and diversification of compounds related to flavor in short-aged cow cheeses.
导言奶酪微生物群非常复杂,由技术相关微生物、腐败微生物、机会性微生物和致病微生物组成。其中主要是乳酸菌和酵母菌。最有趣的乳制品酵母菌之一是马氏雪酪酵母菌,因为它具有技术特性,包括产生香味化合物的能力。通过接种马氏酵母菌 FM09 和商业干酪乳酸酶杆菌菌株的共培养物来制备实验奶酪,并与只接种干酪乳酸酶杆菌的奶酪进行比较。总成分由 FoodScan™ 2 乳制品分析仪测定,游离氨基酸与镉-茚三酮反应后在 507 纳米波长下进行评估。通过顶空固相微萃取法提取挥发性有机化合物,并通过气相色谱-质谱联用臭气活性值进行分析。结果接种马氏酵母菌会导致奶酪的 pH 值升高,蛋白质含量降低,这与在这些奶酪中检测到的较强的蛋白质分解作用一致。马氏酵母菌对香味化合物的含量有定量和定性的影响。特别是观察到醇类、酯类和有机酸的含量增加。此外,有 12 种化合物仅在联合培养获得的奶酪中检测到。这些差异与气味活性值(OAV)一致。事实上,在使用商业菌株的奶酪中,只有 11 种化合物显示出 OAV &gt; 1,而在使用共培养菌株的奶酪中,有 24 种化合物显示出 OAV &gt; 1。qPCR 分析表明 ATF1、EAT1 和 IAH1 基因过度表达。
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引用次数: 0
Impact of weight variation on the microbiome of yak dams and calves 体重变化对牦牛母牛和小牛微生物群的影响
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1465992
Hongzhuang Wang, Wangdui Basang, Zhandui Pingcuo, Nan Jiang, Guangming Sun, Shah Nawaz, Yangji Cidan, Yang Liu, Yanbin Zhu, Dunzhu Luosang
IntroductionLimited information exists regarding the microbiome composition of yak calves of varying weights. Therefore, this study aimed to investigate the microbiomes of mother-calf pairs with different weight profiles.MethodsFecal and blood samples were collected from both lower-weight (CB) and higher-weight (HB) yak calves, along with their corresponding female yaks (CA, HA).ResultsThe results revealed significantly higher levels of T-AOC (total antioxidant capacity) and GSH-Px (glutathione peroxidase) in HB animals (p &lt; 0.001). Sequencing yielded 652,181 and 643,369 filtered reads in female and calf yaks, respectively. Alpha diversity analysis indicated that Chao1, Faith_pd, and Observed species were significantly higher in CA compared to HA (p &lt; 0.01). Furthermore, nine genera were notably different between HA and CA yaks, including Avispirillum, Fimenecus, CAG-1031, Odoribacter 865974, and Jeotgalicoccus A 310962. Compared to CB yaks, CA animals exhibited significant differences in one phylum and six genera, including CAG-485 (p &lt; 0.05), CAG-83 (p &lt; 0.01), Copromorpha (p &lt; 0.01), Phocaeicola A 858004 (p &lt; 0.05), and UBA2253 (p &lt; 0.05).ConclusionIn summary, higher-weight yak calves demonstrated increased oxidative resistance, and weight profiles were linked to the microbiomes of both female yaks and their calves. These findings offer valuable insights for optimizing yak breeding practices in high-altitude regions.
引言 有关不同体重的牦牛犊微生物组组成的信息有限。方法收集体重较轻(CB)和体重较重(HB)的牦牛犊及其相应母牦牛(CA、HA)的粪便和血液样本。结果结果显示,HB动物的T-AOC(总抗氧化能力)和GSH-Px(谷胱甘肽过氧化物酶)水平显著较高(p&;lt;0.001)。母牦牛和小牦牛的测序结果分别为 652,181 和 643,369 个过滤读数。α多样性分析表明,与HA相比,CA中的Chao1、Faith_pd和Observed物种明显较多(p&;lt; 0.01)。此外,HA牦牛和CA牦牛有9个属存在明显差异,包括Avispirillum、Fimenecus、CAG-1031、Odoribacter 865974和Jeotgalicoccus A 310962。与 CB 型牦牛相比,CA 型牦牛在 1 个门和 6 个属中表现出显著差异,包括 CAG-485 (p &lt; 0.05)、CAG-83 (p &lt; 0.01)、Copromorpha (p &lt; 0.01)、Phocaeicola A 858004 (p &lt; 0. 05) 和 UBA2253。结论总之,体重较高的牦牛犊表现出更强的抗氧化能力,体重特征与母牦牛及其犊牛的微生物组有关。这些发现为优化高海拔地区的牦牛饲养方法提供了宝贵的见解。
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引用次数: 0
Iodate reduction by marine aerobic bacteria 海洋好氧菌的碘酸盐还原作用
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1446596
Ken Kine, Shigeki Yamamura, Seigo Amachi
Iodate reductase (Idr) gene cluster (idrABP1P2) is involved in bacterial iodate (IO3) respiration under anaerobic conditions. Putative idr gene clusters are present in both anaerobic and aerobic bacteria; however, the specific physiological roles of idr genes in aerobic bacteria remain unclear. Therefore, in this study, three marine aerobic bacteria with putative idr gene clusters (Roseovarius azorensis, Notoacmeibacter marinus, and Aliiroseovarius sediminilitoris) were grown in the presence of iodate to determine whether they can reduce iodate to iodide (I). All tested bacteria almost completely reduced 2 mM iodate under static conditions but only reduced 0.1–0.5 mM iodate under shaking conditions. Moreover, the washed cell suspension of R. azorensis reduced iodate only when the cells were pre-grown statically in the presence of iodate. Transcriptional analysis revealed that the expression levels of idrA, idrB, idrP1, and idrP2 genes were upregulated in R. azorensis when the cells were grown statically in the presence of iodate. Specifically, idrA expression was induced by 0.1 μM iodate and was up to 14-fold higher compared to that of the non-iodate control. These results suggest that marine aerobic bacteria reduce iodate under oxygen-limited conditions, and that this capacity is induced by environmentally relevant levels of iodate in seawater. Our results suggest that marine aerobic bacteria contribute to iodide production in marine surface waters, thereby affecting the global iodine cycling and ozone budget.
碘酸还原酶(Idr)基因簇(idrABP1P2)参与厌氧条件下细菌的碘酸盐(IO3-)呼吸。厌氧细菌和需氧细菌中都存在推定的 idr 基因簇;然而,idr 基因在需氧细菌中的具体生理作用仍不清楚。因此,本研究在碘酸盐存在下培养了三种具有推定 idr 基因簇的海洋需氧细菌(Roseovarius azorensis、Notoacmeibacter marinus 和 Aliiroseovarius sediminilitoris),以确定它们是否能将碘酸盐还原为碘化物(I-)。在静态条件下,所有测试细菌几乎都能完全还原 2 mM 碘酸盐,但在振荡条件下只能还原 0.1-0.5 mM 碘酸盐。此外,R. azorensis 的水洗细胞悬浮液只有在细胞预先在碘酸盐存在下静态生长时才能还原碘酸盐。转录分析表明,当 R. azorensis 细胞在碘酸盐存在下静态生长时,idrA、idrB、idrP1 和 idrP2 基因的表达水平上调。具体来说,0.1 μM 碘酸盐会诱导 idrA 的表达,与无碘酸盐对照组相比,idrA 的表达量最多可增加 14 倍。这些结果表明,海洋需氧细菌能在限氧条件下还原碘酸根,而海水中环境相关水平的碘酸根能诱导这种能力。我们的研究结果表明,海洋好氧菌有助于海洋表层水碘化物的生成,从而影响全球碘循环和臭氧预算。
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引用次数: 0
Insight into the emerging insect to human pathogen Photorhabdus revealing geographic differences in immune cell tropism 洞察新出现的昆虫致人类病原体光照蝇,揭示免疫细胞向性的地域差异
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1425909
Max Addison, Alexia Hapeshi, Zi Xin Wong, John E. Connolly, Nicholas Robin Waterfield
BackgroundPhotorhabdus asymbiotica is a species of the insect pathogenic Photorhabdus genus that has been isolated as an etiological agent in human infections. Since then, multiple isolates have been identified worldwide; however, actual clinical infections have so far only been identified in North America, Australia, and Nepal. Previous research on the clinical isolates had shown that the strains differed in their behaviour when infecting cultured human cells.MethodsIn this study, we investigate the differences between the pathogenic activities of P. asymbiotica isolates from different geographic locations. Pathogenicity was analysed using infection assays with both cultured cell lines (THP-1, CHO, and HEK cells) and primary immune cells, and peripheral blood mononuclear cells (PBMCs) isolated from human blood.ResultsHere, we present the findings from the Australian (Kingscliff) and North American (ATCC43949) clinical isolates, and non-clinical soilborne nematode isolates from Thailand (PB68) and Northern Europe (HIT and JUN) of P. asymbiotica. We also show the first findings from a new clinical isolate of P. luminescens (Texas), the first non-asymbiotica species to cause a human infection, confirming its ability to infect and survive inside human immune cells.ConclusionHere for the first time, we show how P. asymbiotica selectively infects certain immune cells while avoiding others and that infectivity varies depending on growth temperature. We also show that the tropism varies depending on the geographic location a strain is isolated from, with only the European HIT and JUN strains lack the ability to survive within mammalian cells in tissue culture.
背景Photorhabdus asymbiotica 是昆虫病原体 Photorhabdus 属中的一个物种,已被分离为人类感染的病原体。从那时起,世界各地发现了多个分离株;但迄今为止,仅在北美、澳大利亚和尼泊尔发现了实际的临床感染病例。以前对临床分离株的研究表明,这些菌株在感染培养的人体细胞时表现各异。结果在此,我们展示了澳大利亚(Kingscliff)和北美(ATCC43949)的临床分离物,以及泰国(PB68)和北欧(HIT 和 JUN)的非临床土壤传播线虫分离物的研究结果。我们还首次展示了一种新的临床分离株 P. luminescens(德克萨斯州)的研究结果,这是首个引起人类感染的非共生菌物种,证实了其感染人类免疫细胞并在其中存活的能力。我们还表明,菌株的滋养能力因其分离自的地理位置而异,只有欧洲 HIT 菌株和 JUN 菌株缺乏在组织培养的哺乳动物细胞内存活的能力。
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引用次数: 0
Cytomegalovirus results in poor graft function via bone marrow-derived endothelial progenitor cells 巨细胞病毒通过骨髓内皮祖细胞导致移植物功能低下
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1463335
Weiran Lv, Ya Zhou, Ke Zhao, Li Xuan, Fen Huang, Zhiping Fan, Yuan Chang, Zhengshan Yi, Hua Jin, Yang Liang, Qifa Liu
IntroductionPoor graft function (PGF), characterized by myelosuppression, represents a significant challenge following allogeneic hematopoietic stem cell transplantation (allo-HSCT) with human cytomegalovirus (HCMV) being established as a risk factor for PGF. However, the underlying mechanism remains unclear. Bone marrow endothelial progenitor cells (BM-EPCs) play an important role in supporting hematopoiesis and their dysfunction contributes to PGF development. We aim to explore the effects of CMV on BM-EPCs and its underlying mechanism.MethodsWe investigated the compromised functionality of EPCs derived from individuals diagnosed with HCMV viremia accompanied by PGF, as well as after infected by HCMV AD 169 strain in vitro, characterized by decreased cell proliferation, tube formation, migration and hematopoietic support, and increased apoptosis and secretion of TGF-β1.ResultsWe demonstrated that HCMV-induced TGF-β1 secretion by BM-EPCs played a dominant role in hematopoiesis suppression in vitro experiment. Moreover, HCMV down-regulates Vitamin D receptor (VDR) and subsequently activates p38 MAPK pathway to promote TGF-β1 secretion by BM-EPCs.DiscussionHCMV could infect BM-EPCs and lead to their dysfunction. The secretion of TGF-β1 by BM-EPCs is enhanced by CMV through the activation of p38 MAPK via a VDR-dependent mechanism, ultimately leading to compromised support for hematopoietic progenitors by BM EPCs, which May significantly contribute to the pathogenesis of PGF following allo-HSCT and provide innovative therapeutic strategies targeting PGF.
导言以骨髓抑制为特征的不良移植物功能(PGF)是异基因造血干细胞移植(allo-HSCT)后面临的重大挑战,而人类巨细胞病毒(HCMV)已被确定为 PGF 的风险因素。然而,其潜在机制仍不清楚。骨髓内皮祖细胞(BM-EPCs)在支持造血过程中发挥着重要作用,其功能障碍是导致 PGF 发生的原因之一。方法我们研究了从伴有 PGF 的 HCMV 病毒血症患者以及体外感染 HCMV AD 169 株后的 EPCs 功能受损的情况,其特点是细胞增殖、管形成、迁移和造血支持能力下降,细胞凋亡和 TGF-β1 分泌增加。结果我们在体外实验中发现,HCMV 诱导的 BM-EPCs 分泌 TGF-β1 在造血抑制中起主导作用。此外,HCMV 下调维生素 D 受体(VDR),进而激活 p38 MAPK 通路,促进 BM-EPCs 分泌 TGF-β1。CMV通过VDR依赖机制激活p38 MAPK,增强BM-EPCs分泌TGF-β1的能力,最终导致BM EPCs对造血祖细胞的支持受损,这可能是异体HSCT后PGF发病的重要原因,并提供了针对PGF的创新治疗策略。
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引用次数: 0
Biochar promotes compost humification by regulating bacterial and fungal communities 生物炭通过调节细菌和真菌群落促进堆肥腐殖化
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1470930
Junying Zhang, Bowen Fan, Liqin Zhao, Changjiang Zhao, Fengjun Yang
IntroductionHumus can be formed during composting through biological pathways, nonetheless, the mechanisms through which bacterial and fungal communities govern the development of humus in compost with the addition of biochar remain uncertain.MethodsIn this study, compost with cow dung and maize stover as feedstock was employed as a control group, and compost with 10% biochar added on top of the feedstock was adopted as a treatment group to investigate the effect of bacterial and fungal communities on humus formation during biochar composting.Results and DiscussionThe results demonstrated that the humic acid content increased by 24.82 and 25.10% at the cooling and maturation stages, respectively, after adding biochar. Besides, the degree of polymerization content in the maturation stage was elevated by 90.98%, which accelerated the humification process of the compost. During the thermophilic and maturity stages, there was a respective increase of 51.34 and 31.40% in reducing sugar content, suggesting that the inclusion of biochar could furnish ample reducing sugar substrate for the Maillard reaction. The addition of biochar reduced the number of humus precursor-associated genera by 35, increased the number of genera involved in humus synthesis by two, and enhanced the stability of the cross-domain network between bacteria and fungi, which confirms that microorganisms contribute to the humification process by decreasing humus precursor consumption as well as increasing humus synthesis with the addition of biochar. Additionally, adding biochar could enhance the humification capacity of the compost pile by dominating the Maillard reaction with reducing sugars as the substrate and strengthening the function of humus synthesis-associated genera. This study enhances our comprehension of the regulatory pathways of biochar in the humification process during composting.
引言 腐殖质可在堆肥过程中通过生物途径形成,然而,细菌和真菌群落是通过什么机制来控制添加生物炭的堆肥中腐殖质的形成的,这一点仍不确定。方法本研究以牛粪和玉米秸秆为原料的堆肥为对照组,在原料上添加 10% 生物炭的堆肥为处理组,研究生物炭堆肥过程中细菌和真菌群落对腐殖质形成的影响。此外,成熟阶段的聚合度含量提高了 90.98%,加速了堆肥的腐殖化过程。在嗜热阶段和成熟阶段,还原糖含量分别增加了 51.34% 和 31.40%,这表明生物炭的加入可以为马氏反应提供充足的还原糖基质。加入生物炭后,与腐殖质前体相关的菌属数量减少了 35 个,参与腐殖质合成的菌属数量增加了 2 个,细菌和真菌之间的跨域网络稳定性增强,这证实了加入生物炭后,微生物通过减少腐殖质前体消耗和增加腐殖质合成来促进腐殖化过程。此外,添加生物炭还能通过主导以还原糖为底物的马氏反应,增强腐殖质合成相关菌属的功能,从而提高堆肥的腐殖化能力。这项研究加深了我们对堆肥过程中生物炭在腐殖化过程中的调节途径的理解。
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引用次数: 0
Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color 口腔拭子作为荷斯坦奶牛瘤胃微生物组直接取样的替代物与样品颜色有关
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1466375
Joseph H. Skarlupka, Madison S. Cox, Andrew J. Steinberger, Dino L. Sbardellati, Jennifer C. McClure, Derek M. Bickhart, Andrew J. Scheftgen, Ibrahim Zuniga-Chaves, Luke A. Wolfe, Eric Paget, Charles Skadron, Nithya Attipetty, Garret Suen
Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up to 70% of the ruminal bacterial community, offering potential for broad-scale population-based studies on the rumen microbiome. The swabs collected from dairy cows often vary widely with respect to sample quality, likely due to several factors such as time of sample collection and cow rumination behavior, which may limit the ability of a given swab to accurately represent the ruminal microbiome. One such factor is the color of the swab, which can vary significantly across different cows. Here, we hypothesize that darker-colored swabs contain more rumen contents, thereby better representing the ruminal bacterial community than lighter-colored swabs. To address this, we collected oral swabs from 402 dairy cows and rumen samples from 13 cannulated cows on a research farm in Wisconsin, United States and subjected them to 16S rRNA sequencing. In addition, given that little is known about the ability of oral swabs to recapitulate the ruminal fungal community, we also conducted ITS sequencing of these samples. To correlate swab color to the microbiota we developed and utilized a novel imaging approach to colorimetrically quantify each swab from a range of light to dark. We found that swabs with increasing darkness scores were significantly associated with increased bacterial alpha diversity (p &lt; 0.05). Lighter swabs exhibited greater variation in their community structure, with many identified amplicon sequence variants (ASVs) categorized as belonging to known bovine oral and environmental taxa. Our analysis of the fungal microbiome found that swabs with increasing darkness scores were associated with decreased alpha diversity (p &lt; 0.05) and were also significantly associated with the ruminal solids fungal community, but not with the ruminal liquid community. Our study refines the utility of oral swabs as a useful proxy for capturing the ruminal microbiome and demonstrates that swab color is an important factor to consider when using this approach for documenting both the bacterial and fungal communities.
使用口腔拭子收集奶牛反刍时胃内容物反刍的残余物,可以复制多达 70% 的瘤胃细菌群落,为基于群体的大规模瘤胃微生物组研究提供了潜力。从奶牛身上采集的拭子在样本质量方面往往存在很大差异,这可能是由于样本采集时间和奶牛反刍行为等多种因素造成的,这些因素可能会限制特定拭子准确代表瘤胃微生物群的能力。其中一个因素就是拭子的颜色,不同奶牛的拭子颜色会有很大差异。在这里,我们假设颜色较深的拭子含有更多的瘤胃内容物,因此比颜色较浅的拭子更能代表瘤胃细菌群落。为此,我们在美国威斯康星州的一个研究农场收集了 402 头奶牛的口腔拭子和 13 头插管奶牛的瘤胃样本,并对它们进行了 16S rRNA 测序。此外,鉴于人们对口腔拭子再现瘤胃真菌群落的能力知之甚少,我们还对这些样本进行了 ITS 测序。为了将拭子的颜色与微生物群联系起来,我们开发并使用了一种新颖的成像方法,对每个拭子从浅色到深色的范围进行比色量化。我们发现,颜色越深的拭子与细菌α多样性的增加有显著关联(pamp &;lt;0.05)。浅色拭子的群落结构差异更大,许多已鉴定的扩增子序列变体(ASV)被归类为已知的牛口腔和环境类群。我们对真菌微生物组的分析发现,拭子的暗度分数越高,α多样性越低(p&;lt; 0.05),而且与瘤胃固体真菌群落显著相关,但与瘤胃液体群落无关。我们的研究完善了口腔拭子作为捕捉瘤胃微生物群的有用替代物的实用性,并证明在使用这种方法记录细菌和真菌群落时,拭子的颜色是一个需要考虑的重要因素。
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引用次数: 0
Combination of in silico and molecular techniques for discrimination and virulence characterization of marine Brucella ceti and Brucella pinnipedialis 将硅学和分子技术结合起来,对海洋布鲁氏菌 ceti 和布鲁氏菌 pinnipedialis 进行鉴别和毒力鉴定
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1437408
Guillaume Girault, Luca Freddi, Maryne Jay, Ludivine Perrot, Alexandre Dremeau, Antoine Drapeau, Sabine Delannoy, Patrick Fach, Acacia Ferreira Vicente, Virginie Mick, Claire Ponsart, Vitomir Djokic
IntroductionMammals are the main hosts for Brucella sp., agents of worldwide zoonosis. Marine cetaceans and pinnipeds can be infected by Brucella ceti and B. pinnipedialis, respectively. Besides classical bacteriological typing, molecular approaches such as MLVA, MLSA, and whole-genome sequencing (WGS) can differentiate these species but are cumbersome to perform.MethodsWe compared the DNA and genome sequences of 12 strains isolated from nine marine mammals, with highly zoonotic B. melitensis, B. abortus, and B. suis, and the publicly available genomes of B. ceti and B. pinnipedialis. In silico pipelines were used to detect the antimicrobial resistance (AMR), plasmid, and virulence genes (VGs) by screening six open-source and one home-made library.Results and discussionOur results show that easier-to-use HRM-PCR, Bruce-ladder, and Suis-ladder can separate marine Brucella sp., and the results are fully concordant with other molecular methods, such as WGS. However, the restriction fragment length polymorphism (RFLP) method cannot discriminate between B. pinnipedialis and B. ceti B1-94-like isolates. MLVA-16 results divided the investigated strains into three clades according to their preferred host, which was confirmed in WGS. In silico analysis did not find any AMR and plasmid genes, suggesting antimicrobial susceptibility of marine Brucella, while the presence of the VGs btpA gene was variable dependent on the clade.ConclusionThe HRM-PCR and Suis-ladder are quick, easy, and cost-effective methods to identify marine Brucella sp. Moreover, in silico genome analyses can give useful insights into the genetic virulence and pathogenicity potential of marine Brucella strains.
导言哺乳动物是布鲁氏菌的主要宿主,布鲁氏菌是全球人畜共患病的病原体。海洋鲸目动物和针足类动物可分别感染 ceti 布鲁氏菌和 B. pinnipedialis 布鲁氏菌。除了传统的细菌学分型外,MLVA、MLSA 和全基因组测序(WGS)等分子方法也能区分这些物种,但操作繁琐。方法我们比较了从 9 种海洋哺乳动物体内分离出的 12 株菌株的 DNA 和基因组序列,以及高度人畜共患的梅毒布鲁氏菌、流产布鲁氏菌和鼠疫布鲁氏菌,以及可公开获得的 ceti 和 pinnipedialis 布鲁氏菌基因组。结果与讨论我们的研究结果表明,使用更简便的 HRM-PCR、Bruce-ladder 和 Suis-ladder 可以分离海洋布鲁氏菌,其结果与其他分子方法(如 WGS)完全一致。然而,限制性片段长度多态性(RFLP)方法不能区分B. pinnipedialis和B. ceti B1-94类分离物。MLVA-16 的结果根据调查菌株的偏好宿主将其分为三个支系,这在 WGS 中得到了证实。结论 HRM-PCR和Suis-ladder是快速、简便且经济有效的鉴定海洋布鲁氏菌的方法,此外,硅基因组分析可为海洋布鲁氏菌菌株的遗传毒性和致病潜力提供有用的信息。
{"title":"Combination of in silico and molecular techniques for discrimination and virulence characterization of marine Brucella ceti and Brucella pinnipedialis","authors":"Guillaume Girault, Luca Freddi, Maryne Jay, Ludivine Perrot, Alexandre Dremeau, Antoine Drapeau, Sabine Delannoy, Patrick Fach, Acacia Ferreira Vicente, Virginie Mick, Claire Ponsart, Vitomir Djokic","doi":"10.3389/fmicb.2024.1437408","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1437408","url":null,"abstract":"IntroductionMammals are the main hosts for <jats:italic>Brucella</jats:italic> sp., agents of worldwide zoonosis. Marine cetaceans and pinnipeds can be infected by <jats:italic>Brucella ceti</jats:italic> and <jats:italic>B. pinnipedialis</jats:italic>, respectively. Besides classical bacteriological typing, molecular approaches such as MLVA, MLSA, and whole-genome sequencing (WGS) can differentiate these species but are cumbersome to perform.MethodsWe compared the DNA and genome sequences of 12 strains isolated from nine marine mammals, with highly zoonotic <jats:italic>B. melitensis</jats:italic>, <jats:italic>B. abortus</jats:italic>, and <jats:italic>B. suis</jats:italic>, and the publicly available genomes of <jats:italic>B. ceti</jats:italic> and <jats:italic>B. pinnipedialis. In silico</jats:italic> pipelines were used to detect the antimicrobial resistance (AMR), plasmid, and virulence genes (VGs) by screening six open-source and one home-made library.Results and discussionOur results show that easier-to-use HRM-PCR, Bruce-ladder, and Suis-ladder can separate marine <jats:italic>Brucella</jats:italic> sp., and the results are fully concordant with other molecular methods, such as WGS. However, the restriction fragment length polymorphism (RFLP) method cannot discriminate between <jats:italic>B. pinnipedialis</jats:italic> and <jats:italic>B. ceti</jats:italic> B1-94-like isolates. MLVA-16 results divided the investigated strains into three clades according to their preferred host, which was confirmed in WGS. <jats:italic>In silico</jats:italic> analysis did not find any AMR and plasmid genes, suggesting antimicrobial susceptibility of marine <jats:italic>Brucella</jats:italic>, while the presence of the VGs <jats:italic>btpA</jats:italic> gene was variable dependent on the clade.ConclusionThe HRM-PCR and Suis-ladder are quick, easy, and cost-effective methods to identify marine <jats:italic>Brucella</jats:italic> sp. Moreover, <jats:italic>in silico</jats:italic> genome analyses can give useful insights into the genetic virulence and pathogenicity potential of marine <jats:italic>Brucella</jats:italic> strains.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Co-expression of endoglucanase and cellobiohydrolase from yak rumen in lactic acid bacteria and its preliminary application in whole-plant corn silage fermentation 牦牛瘤胃中的内切葡聚糖酶和纤维素水解酶在乳酸菌中的共表达及其在全株玉米青贮发酵中的初步应用
IF 5.2 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.3389/fmicb.2024.1442797
Xuerui Wan, Yongjie SunKang, Yijun Chen, Zhao Zhang, Huitian Gou, Yu Xue, Chuan Wang, Yaqin Wei, Yuze Yang
IntroductionEndoglucanase (EG) and cellobiohydrolase (CBH) which produced by microorganisms, have been widely used in industrial applications.MethodsIn order to construct recombinant bacteria that produce high activity EG and CBH, in this study, <jats:italic>eg</jats:italic> (endoglucanase) and <jats:italic>cbh</jats:italic> (cellobiohydrolase) were cloned from the rumen microbial genome of yak and subsequently expressed independently and co-expressed within <jats:italic>Lactococcus lactis</jats:italic> NZ9000 (<jats:italic>L. lactis</jats:italic> NZ9000).ResultsThe recombinant strains <jats:italic>L. lactis</jats:italic> NZ9000/pMG36e-usp45-<jats:italic>cbh</jats:italic> (<jats:italic>L. lactis</jats:italic>-<jats:italic>cbh</jats:italic>), <jats:italic>L. lactis</jats:italic> NZ9000/pMG36e-usp45-<jats:italic>eg</jats:italic> (<jats:italic>L. lactis</jats:italic>-<jats:italic>eg</jats:italic>), and <jats:italic>L. lactis</jats:italic> NZ9000/pMG36e-usp45-<jats:italic>eg</jats:italic>-usp45-<jats:italic>cbh</jats:italic> (<jats:italic>L. lactis</jats:italic>-<jats:italic>eg</jats:italic>-<jats:italic>cbh</jats:italic>) were successfully constructed and demonstrated the ability to secrete EG, CBH, and EG-CBH. The sodium carboxymethyl cellulose activity of the recombinant enzyme EG was the highest, and the regenerated amorphous cellulose (RAC) was the specific substrate of the recombinant enzyme CBH, and EG-CBH. The optimum reaction temperature of the recombinant enzyme CBH was 60°C, while the recombinant enzymes EG and EG-CBH were tolerant to higher temperatures (80°C). The optimum reaction pH of EG, CBH, and EG-CBH was 6.0. Mn<jats:sup>2+</jats:sup>, Fe<jats:sup>2+</jats:sup>, Cu<jats:sup>2+</jats:sup>, and Co<jats:sup>2+</jats:sup> could promote the activity of CBH. Similarly, Fe<jats:sup>2+</jats:sup>, Ba<jats:sup>2+</jats:sup>, and higher concentrations of Ca<jats:sup>2+</jats:sup>, Cu<jats:sup>2+</jats:sup>, and Co<jats:sup>2+</jats:sup> could promote the activity of EG-CBH. The addition of engineered strains to whole-plant corn silage improved the nutritional quality of the feed, with the lowest pH, acid detergent fiber (ADF), and neutral detergent fiber (NDF) contents observed in silage from the <jats:italic>L. lactis-eg</jats:italic> group (<jats:italic>p</jats:italic> &lt; 0.05), and the lowest ammonia nitrogen (NH<jats:sub>3</jats:sub>-N), and highest lactic acid (LA) and crude protein (CP) contents in silage from the <jats:italic>L. lactis-eg</jats:italic> + <jats:italic>L. lactis-cbh</jats:italic> group (<jats:italic>p</jats:italic> &lt; 0.05), while the silage quality in the <jats:italic>L. lactis</jats:italic>-<jats:italic>cbh</jats:italic> group was not satisfactory.DiscussionConsequently, the recombinant strains <jats:italic>L. lactis-cbh</jats:italic>, <jats:italic>L. lactis-eg</jats:italic>, and <jats:italic>L. lactis-eg-cbh</jats:italic> were successfully constructed, which could successfully expressed EG, CBH, and EG-CB
方法 为了构建能产生高活性 EG 和 CBH 的重组菌,本研究从牦牛瘤胃微生物基因组中克隆了 EG(内切葡聚糖酶)和 CBH(纤维素水解酶),并在乳球菌 NZ9000(L. lactococcus lactis NZ9000)中进行了独立表达和共表达。结果重组菌株 L. lactis NZ9000/pMG36e-usp45-cbh(L. lactis-cbh)、L. lactis NZ9000/pMG36e-usp45-eg(L. lactis-eg)和 L. lactis NZ9000/pMG36e-usp45-cbh(L. lactis-cbh)在牦牛瘤胃微生物基因组中分别独立表达和共同表达。成功构建了 L. lactis NZ9000/pMG36e-usp45-eg-usp45-cbh(L. lactis-eg-cbh),并证明了其分泌 EG、CBH 和 EG-CBH 的能力。重组酶 EG 的羧甲基纤维素钠活性最高,再生无定形纤维素(RAC)是重组酶 CBH 和 EG-CBH 的特异性底物。重组酶 CBH 的最佳反应温度为 60°C,而重组酶 EG 和 EG-CBH 可耐受更高的温度(80°C)。EG、CBH 和 EG-CBH 的最佳反应 pH 值为 6.0。Mn2+、Fe2+、Cu2+ 和 Co2+ 可促进 CBH 的活性。同样,Fe2+、Ba2+ 以及较高浓度的 Ca2+、Cu2+ 和 Co2+ 可促进 EG-CBH 的活性。在全株玉米青贮中添加工程菌株可改善饲料的营养质量,在 L. lactis-eg 组的青贮中观察到最低的 pH 值、酸性洗涤纤维(ADF)和中性洗涤纤维(NDF)含量(p &p;lt;0.05),在 L. lactis-eg + L. lactis-eg 组的青贮中观察到最低的氨氮(NH3-N)、最高的乳酸(LA)和粗蛋白(CP)含量。讨论成功构建了重组菌株 L. lactis-cbh、L. lactis-eg 和 L. lactis-eg-cbh,它们能成功表达 EG、CBH 和 EG-CBH。L.lactis-eg通过降解纤维素产生糖来促进青贮发酵,从而实现了EG、CBH和EG-CBH的分泌表达,在纤维素降解方面具有潜在的工业应用价值。
{"title":"Co-expression of endoglucanase and cellobiohydrolase from yak rumen in lactic acid bacteria and its preliminary application in whole-plant corn silage fermentation","authors":"Xuerui Wan, Yongjie SunKang, Yijun Chen, Zhao Zhang, Huitian Gou, Yu Xue, Chuan Wang, Yaqin Wei, Yuze Yang","doi":"10.3389/fmicb.2024.1442797","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1442797","url":null,"abstract":"IntroductionEndoglucanase (EG) and cellobiohydrolase (CBH) which produced by microorganisms, have been widely used in industrial applications.MethodsIn order to construct recombinant bacteria that produce high activity EG and CBH, in this study, &lt;jats:italic&gt;eg&lt;/jats:italic&gt; (endoglucanase) and &lt;jats:italic&gt;cbh&lt;/jats:italic&gt; (cellobiohydrolase) were cloned from the rumen microbial genome of yak and subsequently expressed independently and co-expressed within &lt;jats:italic&gt;Lactococcus lactis&lt;/jats:italic&gt; NZ9000 (&lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt; NZ9000).ResultsThe recombinant strains &lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt; NZ9000/pMG36e-usp45-&lt;jats:italic&gt;cbh&lt;/jats:italic&gt; (&lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt;-&lt;jats:italic&gt;cbh&lt;/jats:italic&gt;), &lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt; NZ9000/pMG36e-usp45-&lt;jats:italic&gt;eg&lt;/jats:italic&gt; (&lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt;-&lt;jats:italic&gt;eg&lt;/jats:italic&gt;), and &lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt; NZ9000/pMG36e-usp45-&lt;jats:italic&gt;eg&lt;/jats:italic&gt;-usp45-&lt;jats:italic&gt;cbh&lt;/jats:italic&gt; (&lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt;-&lt;jats:italic&gt;eg&lt;/jats:italic&gt;-&lt;jats:italic&gt;cbh&lt;/jats:italic&gt;) were successfully constructed and demonstrated the ability to secrete EG, CBH, and EG-CBH. The sodium carboxymethyl cellulose activity of the recombinant enzyme EG was the highest, and the regenerated amorphous cellulose (RAC) was the specific substrate of the recombinant enzyme CBH, and EG-CBH. The optimum reaction temperature of the recombinant enzyme CBH was 60°C, while the recombinant enzymes EG and EG-CBH were tolerant to higher temperatures (80°C). The optimum reaction pH of EG, CBH, and EG-CBH was 6.0. Mn&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, Fe&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, Cu&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, and Co&lt;jats:sup&gt;2+&lt;/jats:sup&gt; could promote the activity of CBH. Similarly, Fe&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, Ba&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, and higher concentrations of Ca&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, Cu&lt;jats:sup&gt;2+&lt;/jats:sup&gt;, and Co&lt;jats:sup&gt;2+&lt;/jats:sup&gt; could promote the activity of EG-CBH. The addition of engineered strains to whole-plant corn silage improved the nutritional quality of the feed, with the lowest pH, acid detergent fiber (ADF), and neutral detergent fiber (NDF) contents observed in silage from the &lt;jats:italic&gt;L. lactis-eg&lt;/jats:italic&gt; group (&lt;jats:italic&gt;p&lt;/jats:italic&gt; &amp;lt; 0.05), and the lowest ammonia nitrogen (NH&lt;jats:sub&gt;3&lt;/jats:sub&gt;-N), and highest lactic acid (LA) and crude protein (CP) contents in silage from the &lt;jats:italic&gt;L. lactis-eg&lt;/jats:italic&gt; + &lt;jats:italic&gt;L. lactis-cbh&lt;/jats:italic&gt; group (&lt;jats:italic&gt;p&lt;/jats:italic&gt; &amp;lt; 0.05), while the silage quality in the &lt;jats:italic&gt;L. lactis&lt;/jats:italic&gt;-&lt;jats:italic&gt;cbh&lt;/jats:italic&gt; group was not satisfactory.DiscussionConsequently, the recombinant strains &lt;jats:italic&gt;L. lactis-cbh&lt;/jats:italic&gt;, &lt;jats:italic&gt;L. lactis-eg&lt;/jats:italic&gt;, and &lt;jats:italic&gt;L. lactis-eg-cbh&lt;/jats:italic&gt; were successfully constructed, which could successfully expressed EG, CBH, and EG-CB","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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Frontiers in Microbiology
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