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Article(id=1226956550133171001, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20250082, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1738684800000, receivedDateStr=2025-02-05, revisedDate=null, revisedDateStr=null, acceptedDate=1750953600000, acceptedDateStr=2025-06-27, onlineDate=1770458837301, onlineDateStr=2026-02-07, pubDate=1756915200000, pubDateStr=2025-09-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1770458837301, onlineIssueDateStr=2026-02-07, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1770458837301, creator=13701087609, updateTime=1770458837301, updator=13701087609, issue=Issue{id=1226956547847275311, tenantId=1146029695717560320, journalId=1192105938417971205, year='2025', volume='65', issue='9', pageStart='3821', pageEnd='4232', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1770458836757, creator=13701087609, updateTime=1770459153781, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1226957877613605816, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1226957877613605817, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=3921, endPage=3934, ext={EN=ArticleExt(id=1226956550384829248, articleId=1226956550133171001, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=QIIME 2-based integrative analysis of the effect of fermented feed on the gut microbiota of different animals, columnId=1192149543992045670, journalTitle=Acta Microbiologica Sinica, columnName=Research Article, runingTitle=null, highlight=null, articleAbstract=

The gut microbiota plays a pivotal role in regulating animal health, and its structure and function can be significantly modulated by fermented feed. However, the lack of cross-species comparative studies has hindered a comprehensive understanding of the universal mechanisms underlying fermented feed-mediated microbial regulation. [Objective] To integrate multi-species data for deciphering cross-species regulatory patterns of fermented feed on gut microbiota and elucidating universal functional optimization and host-specific mechanisms. [Methods] We aggregated 464 gut microbiome datasets from pigs, cattle, chickens, and geese. The alpha/beta diversity analyses, linear discriminant analysis effect size (LEfSe), BugBase, and network analyses were employed to assess the diversity, differentially enriched genera, pathogenicity, and interactions of the gut microbiota. [Results] Fermented feed markedly reduced the alpha diversity of gut microbiota in monogastric animals (pigs, chickens, and geese) but not in ruminants (cattle). Although the beta diversity of gut microbiota remained statistically stable in different animals, fermented feed enriched probiotics (e.g., Lactobacillus and Faecalibacterium) while suppressing pathogens (e.g., Campylobacter and Brachyspira) to significantly diminish the pathogenic potential. Network analysis revealed enhanced connectivity, increased network density, reduced modularity, and improved community synergy in fermented feed groups. Host-specific responses were identified: Lactobacillus dominated in pigs, Akkermansia in cattle, and Flavonifractor in chickens. [Conclusion] Fermented feed modulates gut microbiota through a pattern coupling consistent response optimization with host-specific responses, selectively enriching keystone taxa to improve the specific function and reduce the pathogenicity. This study provides theoretical foundations for developing host-tailored fermented feed strategies.

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*E-mail:
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#These authors contributed equally to this work.

, authorsList=Xiaozhong ZHONG, Haolin ZHANG, Mingxi HU, Tao XU, Xiaotong LIU, Wanhao HU, Xinyu ZHANG, Rui ZHOU, Shuhan LEI), CN=ArticleExt(id=1226956557997491171, articleId=1226956550133171001, tenantId=1146029695717560320, journalId=1192105938417971205, language=CN, title=QIIME 2整合分析发酵饲料对不同动物肠道微生物群落的影响, columnId=1192149544164012138, journalTitle=微生物学报, columnName=研究报告, runingTitle=null, highlight=null, articleAbstract=

肠道微生物群落是调控动物健康的关键因素，其结构和功能可被发酵饲料显著影响。然而，目前缺乏跨物种比较研究，限制了对发酵饲料共性调控机制的理解。 【目的】 整合多物种数据，解析发酵饲料对肠道菌群的跨物种调控规律，揭示功能优化的普遍性与宿主特异性机制。 【方法】 整合猪、牛、鸡、鹅的464个肠道微生物组数据，分别采用α/β多样性、线性判别效应分析(linear discriminant analysis effect size, LEfSe)、BugBase及网络分析，评估发酵饲料组和对照组间的肠道微生物多样性、差异菌属、潜在致病性和互作关系。 【结果】 发酵饲料显著降低了单胃动物(猪、鸡、鹅)肠道微生物的α多样性；不同动物肠道微生物群落的β多样性无显著变化，但发酵饲料组显著富集益生菌[如乳杆菌属(Lactobacillus)和粪杆菌属(Faecalibacterium)]，抑制了致病菌[如弯曲杆菌属(Campylobacter)、短螺菌属(Brachyspira)]，潜在致病性降低。网络分析显示发酵饲料组的连接度、网络密度提高，模块化降低，群落协同性增强。物种特异性分析表明，猪、牛、鸡分别富集了乳杆菌属(Lactobacillus)、阿克曼氏菌属(Akkermansia)、解黄酮菌属(Flavonifractor)等不同的益生菌，体现了宿主特异性响应。 【结论】 发酵饲料通过共性响应优化结合物种特异性响应模式调控肠道菌群，选择性富集关键菌群以增强特定功能、降低致病性，为发酵饲料共性技术的开发提供理论依据。

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作者贡献声明

钟小忠：提出概念、监督管理、稿件润色修改；张昊霖：初稿写作；胡明茜：收集和管理猪肠道微生物数据；许涛：收集和管理牛肠道微生物数据；刘晓彤：文献收集和整理；胡莞浩：收集和管理鸡肠道微生物数据；张馨予：收集和管理鹅肠道微生物数据；周瑞：数据分析；雷舒涵：数据可视化。

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Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future[J]. Frontiers in Microbiology, 2018, 9: 2161., articleTitle=Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future, refAbstract=null), Reference(id=1226964068699910457, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, doi=null, pmid=null, pmcid=null, year=2024, volume=15, issue=1, pageStart=25, pageEnd=null, url=null, language=null, rfNumber=[45], rfOrder=47, authorNames=GAO MK, LIAO CY, FU JY, NING ZH, LV ZP, GUO YM, journalName=Journal of Animal Science and Biotechnology, refType=null, unstructuredReference=GAO MK, LIAO CY, FU JY, NING ZH, LV ZP, GUO YM. Probiotic cocktails accelerate baicalin metabolism in the ileum to modulate intestinal health in broiler chickens[J]. Journal of Animal Science and Biotechnology, 2024, 15(1): 25., articleTitle=Probiotic cocktails accelerate baicalin metabolism in the ileum to modulate intestinal health in broiler chickens, refAbstract=null)], funds=[Fund(id=1226964059568911318, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, awardId=2024NB04, language=EN, fundingSource=National Engineering Research Center of Solid-state Brewing Funding Project(2024NB04), fundOrder=null, country=null), Fund(id=1226964059682157533, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, awardId=2024NB04, language=CN, fundingSource=国家固态酿造工程技术研究中心资助项目(2024NB04), fundOrder=null, country=null), Fund(id=1226964059820569574, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, awardId=S202410626059, language=EN, fundingSource=Sichuan Provincial College Student Innovation Training Program(S202410626059), fundOrder=null, country=null), Fund(id=1226964059942204399, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, awardId=S202410626059, language=CN, fundingSource=四川省大学生创新训练计划(S202410626059), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1226964048047157565, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, xref=null, ext=[AuthorCompanyExt(id=1226964048055546175, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048047157565, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 College of Life Sciences, Sichuan Agricultural University, Ya’an, Sichuan, China), AuthorCompanyExt(id=1226964048072323392, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048047157565, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 四川农业大学 生命科学学院，四川 雅安)]), AuthorCompany(id=1226964048177180998, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, xref=null, ext=[AuthorCompanyExt(id=1226964048189763912, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048177180998, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 College of Bioengineering, Chongqing University, Chongqing, China), AuthorCompanyExt(id=1226964048240095567, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048177180998, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 重庆大学 生物工程学院，重庆)]), AuthorCompany(id=1226964048353341783, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, xref=null, ext=[AuthorCompanyExt(id=1226964048365924697, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048353341783, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3 Luzhou Laojiao Co. , Ltd. , Luzhou, Sichuan, China), AuthorCompanyExt(id=1226964048382701915, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048353341783, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3 泸州老窖股份有限公司，四川 泸州)]), AuthorCompany(id=1226964048495948127, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, xref=null, ext=[AuthorCompanyExt(id=1226964048508531040, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048495948127, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=4 National Engineering Research Center of Solid-state Brewing, Luzhou, Sichuan, China), AuthorCompanyExt(id=1226964048533696866, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, companyId=1226964048495948127, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=4 国家固态酿造工程技术研究中心，四川 泸州)])], figs=[ArticleFig(id=1226964056200885046, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Figure 1, caption=Distribution of alpha diversity indices of gut microbiota in different animals. A: Chao1 index; B: ACE index; C: Shannon index; D: Simpson index. ****: P<0.000 1; ***: P<0.001; **: P<0.01; *: P<0.05., figureFileSmall=+qOpBWRvDIQ3iP9+p95p+A==, figureFileBig=5PToiwbcCHFoLSnLfvkjbQ==, tableContent=null), ArticleFig(id=1226964056305742653, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=图1, caption=不同动物肠道菌群α多样性指数分布。A：Chao1指数；B：ACE指数；C：Shannon指数；D：Simpson指数。, figureFileSmall=+qOpBWRvDIQ3iP9+p95p+A==, figureFileBig=5PToiwbcCHFoLSnLfvkjbQ==, tableContent=null), ArticleFig(id=1226964056439960397, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Figure 2, caption=NMDS distribution of gut microbiota in different animals. A: All animals; B: Pigs; C: Cattles; D: Chickens; E: Geese., figureFileSmall=HFWtTQ5MMy4FBY23d8Vx0w==, figureFileBig=R3B8sjwQivzbO+rvFskvPA==, tableContent=null), ArticleFig(id=1226964056574178133, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=图2, caption=不同动物肠道菌群NMDS分布。A：所有考察动物；B：猪；C：牛；D：鸡；E：鹅。, figureFileSmall=HFWtTQ5MMy4FBY23d8Vx0w==, figureFileBig=R3B8sjwQivzbO+rvFskvPA==, tableContent=null), ArticleFig(id=1226964056670647133, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Figure 3, caption=Distribution of abundant genera in different animals., figureFileSmall=mMo9LhaBXz4FQOPQfzUaNQ==, figureFileBig=+x+6AHfeoaQiq/q5VhPBCw==, tableContent=null), ArticleFig(id=1226964056779699044, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=图3, caption=不同动物肠道菌群的优势菌属分布, figureFileSmall=mMo9LhaBXz4FQOPQfzUaNQ==, figureFileBig=+x+6AHfeoaQiq/q5VhPBCw==, tableContent=null), ArticleFig(id=1226964056871973743, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Figure 4, caption=Dominant genera in the gut microbiota of different animals that show significant differences (LDA>2). A: All animals; B: Pigs; C: Cattles; D: Chickens; E: Geese., figureFileSmall=3pTrAdkHiRH6fNb7/nAC6A==, figureFileBig=VmHRxEftiNn55CwTbef9/A==, tableContent=null), ArticleFig(id=1226964056955859829, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=图4, caption=不同动物肠道菌群优势菌属中具有显著差异(LDA>2)的菌属。A：所有考察动物；B：猪；C：牛；D：鸡；E：鹅。, figureFileSmall=3pTrAdkHiRH6fNb7/nAC6A==, figureFileBig=VmHRxEftiNn55CwTbef9/A==, tableContent=null), ArticleFig(id=1226964057060717437, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Figure 5, caption=Potential pathogenicity of animal gut microbiota and its association with alpha diversity indices. A: Potential pathogenicity indices across different animals; B: Linear regression model between Chao1 index and potential pathogenicity in all animals; C: Linear regression model between Shannon index and potential pathogenicity in all animals. ***: P<0.001; **: P<0.01; *: P<0.05; ns: Not significant., figureFileSmall=q+i/Pdeb0H3o9aSUyxslDg==, figureFileBig=U2e5cU+d00Li8H8p63W7Hw==, tableContent=null), ArticleFig(id=1226964057203323784, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=图5, caption=动物肠道菌群潜在致病性及其与α多样性指数的关系。A：不同动物的潜在致病性指数；B：所有考察动物中Chao1指数和潜在致病性的线性回归模型；C：所有考察动物中Shannon指数和潜在致病性的线性回归模型。, figureFileSmall=q+i/Pdeb0H3o9aSUyxslDg==, figureFileBig=U2e5cU+d00Li8H8p63W7Hw==, tableContent=null), ArticleFig(id=1226964057320764305, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Figure 6, caption=Network analysis of the gut microbiota at the overall level for all animals. Genera with degree>10 are marked in the network. A: Network of the control group; B: Network of the fermented feed group; C: Key species analysis of the control group network; D: Key species analysis of the FF group network., figureFileSmall=6Zfg1x9yDM3oafghASmV6w==, figureFileBig=JGpLzwzsU4l6j0uOpBPKQQ==, tableContent=null), ArticleFig(id=1226964057446593434, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=图6, caption=所有考察动物整体水平的网络分析。网络中标注属名的为连接度大于10的菌属。A：对照组网络；B：发酵饲料组网络；C：对照组网络关键物种分析；D：发酵饲料组网络关键物种分析。, figureFileSmall=6Zfg1x9yDM3oafghASmV6w==, figureFileBig=JGpLzwzsU4l6j0uOpBPKQQ==, tableContent=null), ArticleFig(id=1226964057614365606, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=EN, label=Table 1, caption=

The information of the data sets analyzed in this study

, figureFileSmall=null, figureFileBig=null, tableContent=
Project number

Primer

region

AnimalsAnimals informationSampling siteFF raw materialSample sizeReferences
FFControl
PRJNA384694V4PigFinishing pigsFecesFeedstuffs147[10]
PRJNA1069293V3-V4PigGrowing pigsFecesFlaxseed meal248[11]
PRJNA725094V3-V4PigUnknownGut contentComplete feed.66[8]
PRJNA891080V3-V4PigPigletsGut contentUnknown1010[12]
PRJNA524989V4-V5PigGrowing pigsGut contentCorn-soybean meal1512[13]
PRJNA787021V3-V4PigUnknownFecesComplete feed33[14]
PRJNA648691V3–V4PigMale pigletsGut contentSoybean meal5712[15]
PRJNA714150V3–V4PigWeaned boarsFecesHerbal mixture3618[16]
PRJNA1091436V3-V4PigWeaned pigletsFecesPurslane88[17]
PRJNA607631V4-V5PigGrowing pigsGut contentCorn-soybean meal1210[18]
PRJNA743130V4-V5PigWeaned pigletGut contentCottonseed meal1212[19]
PRJEB27667V3-V4PigUnknownGut contentMao-tai lees186[20]
PRJNA1047959V3-V4GooseXianghai geeseGut contentMaize stover66[21]
PRJNA492962V3-V4GooseYangzhou geeseGut contentUnknown186[22]
PRJNA858635V3-V4ChickenBroilersGut contentGrape seed meal3612[23]
PRJNA1028111V3-V4ChickenChahua chickensGut contentSoybean hulls:rapeseed cake155[24]
PRJNA533918V4ChickenGray hensGut contentUnknown3612[25]
PRJNA669464V3-V4CattleHolstein cowsRumen content and fecesCorn gluten-wheat bran mixture3618[26]
PRJNA472376V4CattleUnknownFecesUnknown1414[27]
PRJNA450498V4-V5CattleSimmental cattleRumen contentRice straw6060[28]
), ArticleFig(id=1226964057798914989, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956550133171001, language=CN, label=表1, caption=

本研究中分析的数据集信息

, figureFileSmall=null, figureFileBig=null, tableContent=
Project number

Primer

region

AnimalsAnimals informationSampling siteFF raw materialSample sizeReferences
FFControl
PRJNA384694V4PigFinishing pigsFecesFeedstuffs147[10]
PRJNA1069293V3-V4PigGrowing pigsFecesFlaxseed meal248[11]
PRJNA725094V3-V4PigUnknownGut contentComplete feed.66[8]
PRJNA891080V3-V4PigPigletsGut contentUnknown1010[12]
PRJNA524989V4-V5PigGrowing pigsGut contentCorn-soybean meal1512[13]
PRJNA787021V3-V4PigUnknownFecesComplete feed33[14]
PRJNA648691V3–V4PigMale pigletsGut contentSoybean meal5712[15]
PRJNA714150V3–V4PigWeaned boarsFecesHerbal mixture3618[16]
PRJNA1091436V3-V4PigWeaned pigletsFecesPurslane88[17]
PRJNA607631V4-V5PigGrowing pigsGut contentCorn-soybean meal1210[18]
PRJNA743130V4-V5PigWeaned pigletGut contentCottonseed meal1212[19]
PRJEB27667V3-V4PigUnknownGut contentMao-tai lees186[20]
PRJNA1047959V3-V4GooseXianghai geeseGut contentMaize stover66[21]
PRJNA492962V3-V4GooseYangzhou geeseGut contentUnknown186[22]
PRJNA858635V3-V4ChickenBroilersGut contentGrape seed meal3612[23]
PRJNA1028111V3-V4ChickenChahua chickensGut contentSoybean hulls:rapeseed cake155[24]
PRJNA533918V4ChickenGray hensGut contentUnknown3612[25]
PRJNA669464V3-V4CattleHolstein cowsRumen content and fecesCorn gluten-wheat bran mixture3618[26]
PRJNA472376V4CattleUnknownFecesUnknown1414[27]
PRJNA450498V4-V5CattleSimmental cattleRumen contentRice straw6060[28]
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QIIME 2整合分析发酵饲料对不同动物肠道微生物群落的影响
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钟小忠 1 , 张昊霖 1 , 胡明茜 1 , 许涛 2, 3 , 刘晓彤 3, 4 , 胡莞浩 1 , 张馨予 1 , 周瑞 1 , 雷舒涵 1
微生物学报 | 研究报告 2025,65(9): 3921-3934
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微生物学报 | 研究报告 2025, 65(9): 3921-3934
QIIME 2整合分析发酵饲料对不同动物肠道微生物群落的影响
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钟小忠1 , 张昊霖1, 胡明茜1, 许涛2, 3, 刘晓彤3, 4, 胡莞浩1, 张馨予1, 周瑞1, 雷舒涵1
作者信息
  • 1 四川农业大学 生命科学学院，四川 雅安
  • 2 重庆大学 生物工程学院，重庆
  • 3 泸州老窖股份有限公司，四川 泸州
  • 4 国家固态酿造工程技术研究中心，四川 泸州
QIIME 2-based integrative analysis of the effect of fermented feed on the gut microbiota of different animals
Xiaozhong ZHONG1 , Haolin ZHANG1, Mingxi HU1, Tao XU2, 3, Xiaotong LIU3, 4, Wanhao HU1, Xinyu ZHANG1, Rui ZHOU1, Shuhan LEI1
Affiliations
  • 1 College of Life Sciences, Sichuan Agricultural University, Ya’an, Sichuan, China
  • 2 College of Bioengineering, Chongqing University, Chongqing, China
  • 3 Luzhou Laojiao Co. , Ltd. , Luzhou, Sichuan, China
  • 4 National Engineering Research Center of Solid-state Brewing, Luzhou, Sichuan, China
出版时间: 2025-09-04 doi: 10.13343/j.cnki.wsxb.20250082
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摘要
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肠道微生物群落是调控动物健康的关键因素，其结构和功能可被发酵饲料显著影响。然而，目前缺乏跨物种比较研究，限制了对发酵饲料共性调控机制的理解。 【目的】 整合多物种数据，解析发酵饲料对肠道菌群的跨物种调控规律，揭示功能优化的普遍性与宿主特异性机制。 【方法】 整合猪、牛、鸡、鹅的464个肠道微生物组数据，分别采用α/β多样性、线性判别效应分析(linear discriminant analysis effect size, LEfSe)、BugBase及网络分析，评估发酵饲料组和对照组间的肠道微生物多样性、差异菌属、潜在致病性和互作关系。 【结果】 发酵饲料显著降低了单胃动物(猪、鸡、鹅)肠道微生物的α多样性；不同动物肠道微生物群落的β多样性无显著变化，但发酵饲料组显著富集益生菌[如乳杆菌属(Lactobacillus)和粪杆菌属(Faecalibacterium)]，抑制了致病菌[如弯曲杆菌属(Campylobacter)、短螺菌属(Brachyspira)]，潜在致病性降低。网络分析显示发酵饲料组的连接度、网络密度提高，模块化降低，群落协同性增强。物种特异性分析表明，猪、牛、鸡分别富集了乳杆菌属(Lactobacillus)、阿克曼氏菌属(Akkermansia)、解黄酮菌属(Flavonifractor)等不同的益生菌，体现了宿主特异性响应。 【结论】 发酵饲料通过共性响应优化结合物种特异性响应模式调控肠道菌群，选择性富集关键菌群以增强特定功能、降低致病性，为发酵饲料共性技术的开发提供理论依据。

发酵饲料  /  养殖动物  /  肠道微生物  /  微生物群落  /  潜在致病性  /  共现性网络

The gut microbiota plays a pivotal role in regulating animal health, and its structure and function can be significantly modulated by fermented feed. However, the lack of cross-species comparative studies has hindered a comprehensive understanding of the universal mechanisms underlying fermented feed-mediated microbial regulation. [Objective] To integrate multi-species data for deciphering cross-species regulatory patterns of fermented feed on gut microbiota and elucidating universal functional optimization and host-specific mechanisms. [Methods] We aggregated 464 gut microbiome datasets from pigs, cattle, chickens, and geese. The alpha/beta diversity analyses, linear discriminant analysis effect size (LEfSe), BugBase, and network analyses were employed to assess the diversity, differentially enriched genera, pathogenicity, and interactions of the gut microbiota. [Results] Fermented feed markedly reduced the alpha diversity of gut microbiota in monogastric animals (pigs, chickens, and geese) but not in ruminants (cattle). Although the beta diversity of gut microbiota remained statistically stable in different animals, fermented feed enriched probiotics (e.g., Lactobacillus and Faecalibacterium) while suppressing pathogens (e.g., Campylobacter and Brachyspira) to significantly diminish the pathogenic potential. Network analysis revealed enhanced connectivity, increased network density, reduced modularity, and improved community synergy in fermented feed groups. Host-specific responses were identified: Lactobacillus dominated in pigs, Akkermansia in cattle, and Flavonifractor in chickens. [Conclusion] Fermented feed modulates gut microbiota through a pattern coupling consistent response optimization with host-specific responses, selectively enriching keystone taxa to improve the specific function and reduce the pathogenicity. This study provides theoretical foundations for developing host-tailored fermented feed strategies.

fermented feed  /  farmed animals  /  gut microbiota  /  microbial communities  /  potential pathogenicity  /  co-occurrence network
钟小忠, 张昊霖, 胡明茜, 许涛, 刘晓彤, 胡莞浩, 张馨予, 周瑞, 雷舒涵. QIIME 2整合分析发酵饲料对不同动物肠道微生物群落的影响. 微生物学报, 2025 , 65 (9) : 3921 -3934 . DOI: 10.13343/j.cnki.wsxb.20250082
Xiaozhong ZHONG, Haolin ZHANG, Mingxi HU, Tao XU, Xiaotong LIU, Wanhao HU, Xinyu ZHANG, Rui ZHOU, Shuhan LEI. QIIME 2-based integrative analysis of the effect of fermented feed on the gut microbiota of different animals[J]. Acta Microbiologica Sinica, 2025 , 65 (9) : 3921 -3934 . DOI: 10.13343/j.cnki.wsxb.20250082
正文
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动物肠道微生物群落在维持宿主健康中发挥重要作用，主要通过营养代谢、免疫调节及屏障保护等途径影响动物生理状态[1-3]。近年来，发酵饲料因能通过微生物代谢生成有机酸、抗菌肽等功能性产物，显著调控肠道菌群组成，已成为动物营养领域的研究热点[4]。现有研究表明，发酵饲料对肠道微生物的影响存在显著物种差异[5]。例如，发酵饲料可显著提升仔鸡肠道乳杆菌属(Lactobacillus)的丰度并抑制脱硫弧菌属(Desulfovibrio)[6]，同时降低仔猪肠道梭菌纲(Clostridia)的比例并富集拟杆菌纲(Bacteroidia)[7]。以上研究表明，发酵饲料的调控效应高度依赖宿主物种特性。
不同动物肠道微生物对发酵饲料的响应模式可能存在共性。已有研究表明，发酵饲料使育肥猪中假单胞菌门(Pseudomonadota)的致病菌减少，而芽孢杆菌门(Bacillota)等有益菌增加[8]；类似地，肉鸡饲喂发酵饲料后，芽孢杆菌门和拟杆菌门(Bacteroidota)的微生物比例增加，而包含多种致病菌的假单胞菌门的比例下降[9]，提示发酵饲料可能对肠道菌群产生跨物种的共性优化效应。尽管发酵饲料的原料、菌种及工艺差异导致微生物组成的物种特异性响应，但其可能通过共性机制驱动益生菌富集和致病菌抑制的跨物种调控。
本研究整合猪、牛、鸡、鹅多物种肠道微生物数据，系统解析发酵饲料的调控规律，揭示跨物种肠道微生物对发酵饲料的共性响应模式，以及发酵饲料对肠道微生物的宿主特异性调控机制，以期为发酵饲料共性技术的开发提供理论依据。
1 材料与方法
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1.1 数据收集与预处理
整合来自美国国家生物技术信息中心(National Center for Biotechnology Information, NCBI)等公共数据库的20项已发表研究，共收集到681个涉及发酵饲料(fermented feed，FF)研究的动物肠道微生物16S rRNA基因扩增子测序样本，涵盖猪(327个样本)、牛(202个样本)、鸡(116个样本)和鹅(36个样本)(表1)。为确保数据可比性，筛选时仅保留具有共同V4测序区段(250 bp)且提供原始fastq文件的研究。序列预处理采用QIIME 2 (v2024.1)分析流程[29]：首先利用cutadapt去除V4区上游引物515F (5′-GTGC CAGCMGCCGCGGTAA-3′)；通过DADA2算法，剔除最大预期错误率(max_ee)>2.0、长度<200 bp的序列，设置前向截断长度为250 bp (--p-trunc-len 250)，去除嵌合体，并生成扩增子序列变体(amplicon sequence variants, ASVs)，保留的序列即为V4区的250 bp序列。为了确保分析可靠性，进一步去除了序列数低于10 000的样本，最终保留了464个(猪258个，牛109个，鸡77个，鹅20个)高质量样本用于后续分析。
1.2 多样性分析与物种注释
样品微生物群落的α多样性分析基于R语言vegan包(v2.6-4)计算Chao1指数、Shannon指数、ACE指数和Simpson指数。β多样性通过Bray-Curtis距离矩阵进行非度量多维尺度分析(non-metric multidimensional scaling, NMDS)，以应力值(stress<0.20)评估降维效果。物种注释通过QIIME feature-classifier与SILVA 138.1数据库(99%相似度阈值)比对进行属水平分类[30]，同时采用Greengenes 13.8数据库分类以支持BugBase表型预测[31]。功能预测通过BugBase (v1.0)实现，评估群落潜在致病性等表型特征[32]。
1.3 差异物种分析
差异菌属鉴定通过线性判别效应分析(linear discriminant analysis effect size, LEfSe)完成：首先利用Kruskal-Wallis检验(P<0.05)筛选组间差异菌属，再以线性判别分析(linear discriminant analysis, LDA)效应量(LDA>2)确定显著性物种，并采用Benjamini-Hochberg法校正多重检验假发现率(false discovery rate, FDR<0.05)[33]。
1.4 微生物互作网络分析
微生物属水平互作网络分析基于分子生态网络分析(molecular ecological network analysis, MENA)平台完成[34]，只保留在至少50%样品中均存在的菌属，以Pearson相关性计算相似性矩阵，计算网络拓扑参数(如连接度、网络密度、模块度等)。关键物种通过模块内连接度(within module connectivity, Zi>2.5)与模块间连接度(among-module connectivity, Pi>0.6)识别，网络可视化使用Gephi软件(v0.9.2)完成[35]。
1.5 统计分析
α多样性组间差异通过Wilcoxon秩和检验进行统计分析，所有统计分析均在R语言环境中完成，显著性水平设为P<0.05。
2 结果与分析
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2.1 发酵饲料对不同动物肠道微生物群落α多样性的影响
发酵饲料组和对照组(control)的肠道微生物α多样性比较分析结果表明，发酵饲料显著降低了猪、鸡和鹅的肠道微生物α多样性。在整体水平上，发酵饲料组的Chao1指数(图1A)、ACE指数(图1B)、Shannon指数(图1C)和Simpson指数(图1D)均显著低于对照组(P<0.05)。
不同物种比较分析显示，发酵饲料对肠道微生物α多样性的影响具有动物特异性。在单胃动物中，猪、鸡和鹅的发酵饲料组较对照组均表现出显著降低Chao1指数、ACE指数、Shannon指数和Simpson指数(P<0.05)。然而，在反刍动物牛中，发酵饲料组与对照组的α多样性指数并无显著差异(P>0.05)。这一结果表明，动物的消化系统特征可能是影响发酵饲料调节肠道微生物多样性的关键因素。
2.2 发酵饲料对不同动物肠道微生物群落β多样性的影响
为评估发酵饲料对不同动物肠道微生物群落结构的整体影响，采用NMDS对其β多样性进行了分析。NMDS模型中的stress值均小于0.20，说明拟合结果较可靠。如图2所示，发酵饲料组和对照组的样本分布基本重叠，不存在显著差异(P>0.05)，表明饲喂发酵饲料并未显著改变所有考察动物的肠道菌群整体结构。
2.3 不同动物肠道微生物群落组成和差异分析
微生物群落组成分析结果显示(图3)，不同动物肠道具有独特的优势菌群特征。在猪肠道菌群中，排名前三的菌属为梭菌属(Clostridium_sensu_stricto_1，9.21% FF/7.32% Control)、乳杆菌属(7.79% FF/5.31% Control)和普雷沃氏菌属(8.43% FF/4.43% Control)；牛肠道菌群中为普雷沃氏菌属(14.00% FF/12.04% Control)、理化所菌科RC9群(Rikenellaceae_RC9_gut_group，7.89% FF/ 7.15% Control)和UCG-005(5.48% FF/5.86% Control)；鸡肠道菌群中，拟杆菌属(Bacteroides，15.84% FF/16.52% Control)、理化所菌科RC9群(6.71% FF/4.34% Control)和粪杆菌属(5.90% FF/4.41% Control)丰度最高；鹅肠道菌群中是拟杆菌属(21.60% FF/18.10% Control)、脱硫弧菌属(9.43% FF/8.13% Control)和粪杆菌属(3.64% FF/3.22% Control)。
为了评估发酵饲料对不同动物肠道微生物组成的具体影响，本研究筛选了每个动物组中排名前50的优势菌属用于LEfSe分析，以P<0.05和LDA>2为阈值划分显著差异的物种(图4)。在门水平上，所有考察动物(图4A)对照组肠道菌群中螺旋体门(Spirochaetota)和拟杆菌门(Bacteroidota)显著富集，发酵饲料组中放线菌门(Actinobacteriota)、脱硫杆状菌门(Desulfobacterota)和芽孢杆菌门显著富集；猪(图4B)对照组中弯曲菌门(Campylobacterota)和拟杆菌门显著富集，发酵饲料组中芽孢杆菌门显著富集；牛(图4C)发酵饲料组中疣微菌门(Verrucomicrobiota)、髌骨菌门(Patescibacteria)和假单胞菌门显著富集；鸡和鹅在门水平上无显著差异。
在属水平上，所有考察动物(图4A)对照组肠道菌群中显著富集的优势菌属包括螺旋体属(Treponema)、厌氧弧菌属(Anaerovibrio)、罗斯拜瑞氏菌属(Roseburia)、拟杆菌目RF16群(Bacteroidales_RF16_group)、异普雷沃菌属(Alloprevotella)、普雷沃菌科UCG-003群(Prevotellaceae_UCG-003)、普雷沃菌科NK3B31群(Prevotellaceae_NK3B31_group)和普雷沃菌属，发酵饲料组显著富集的优势属包括欧尔森氏菌属(Olsenella)、脱硫弧菌属、Colidextribacter、瘤胃球菌属([Ruminococcus]_torques_group)、梭菌纲UCG-014群(Clostridia_UCG-014)、粪杆菌属和乳杆菌属；猪(图4B)对照组显著富集的优势属包括考拉杆菌属(Phascolarctobacterium)、弯曲杆菌属、厌氧弧菌属、罗斯拜瑞氏菌属、拟杆菌目RF16群(Bacteroidales_RF16_group)、普雷沃菌科UCG-003群、异普雷沃菌属和普雷沃菌属，发酵饲料组显著富集的优势属包括梭菌纲UCG-014群(Clostridia_UCG-014)和乳杆菌属；牛(图4C)对照组显著富集的优势属为琥珀酸弧菌科UCG-001群(Succinivibrionaceae_UCG-001)，发酵饲料组显著富集的优势属包括阿克曼菌属、琥珀酸弧菌科UCG-002群(Succinivibrionaceae_UCG-002)和假丁酸弧菌属(Pseudobutyrivibrio)；鸡(图4D)对照组显著富集的优势属包括克里斯滕森氏菌科R-7群(Christensenellaceae_R-7_group)、乳杆菌属和Candidatus_Arthromitus，发酵饲料组显著富集的优势属包括解黄酮菌属、苏黎世杆菌属(Turicibacter)；鹅(图4E)对照组显著富集的优势属包括短螺菌属、红斑丹Erysipelatoclostridium、消化球菌属(Peptococcus)、罕见小球菌属(Subdoligranulum)和理化所菌科RC9群，发酵饲料组显著富集的优势属包括Gastranaerophilales和UCG-005。
2.4 发酵饲料对不同动物肠道微生物群落潜在致病性的影响
通过BugBase表型预测分析了不同动物肠道菌群的潜在致病性(图5A)，结果表明发酵饲料组显著降低了所有考察动物、猪、牛和鹅肠道菌群的潜在致病性。具体而言，所有考察动物对照组和发酵饲料组的潜在致病性分别为0.54±0.14和0.44±0.15；猪对照组和发酵饲料组分别为0.51±0.14和0.47±0.13；牛对照组和发酵饲料组分别为0.59±0.14和0.54±0.13；鹅对照组和发酵饲料组分别为0.50±0.08和0.41±0.09；而鸡对照组和发酵饲料组的潜在致病性分别为0.49±0.12和0.44±0.14。进一步对所有考察动物肠道菌群α多样性和潜在致病性指数进行线性回归分析发现，Chao1指数(R2=0.21，P<0.001，图5B)和Shannon指数(R2=0.16，P<0.001，图5C)均与潜在致病性呈显著正相关。这一结果表明，肠道微生物群落多样性的降低可能导致了肠道菌群潜在致病性降低。
2.5 发酵饲料对动物肠道微生物群落分子生态网络的影响
对所有考察动物的对照组(图6A)和发酵饲料组(图6B)进行微生物网络分析(表2)表明，发酵饲料组(68个节点)较对照组(78个节点)具有更少的节点数，但表现出更多的连接数(278 vs.206)和更高的平均连接度(8.17 vs.5.28)。发酵饲料组的网络密度(0.12 vs. 0.07)也高于对照组，表明发酵饲料组菌群间的相互作用更为紧密。在关键节点方面，对照组中仅有5个菌属的连接度大于10，分别为F082、Defluviitaleaceae_UCG-011、别样杆菌属(Alistipes)、毛螺菌科UCG-010群(Lachnospiraceae_UCG-010)和丁酸球菌属(Butyricicoccus)，而发酵饲料组中有15个菌属的连接度超过10，其中别样杆菌属、副萨特氏菌属(Parasutterella)和F082为连接度最高的3个属，表明发酵饲料组中具有更多的互作菌群。模块化分析显示，对照组和发酵饲料组分别形成4个和3个模块，对照组的模块度(0.36)高于发酵饲料组(0.24)。
进一步通过Zi (模块内连接)和Pi (模块间连接)值计算分析了网络中的关键物种。在对照组中(图6C)，共鉴定出11个关键物种，包括1个网络枢纽物种(network hubs，F082)、1个模块枢纽物种别样杆菌属和9个连接物种，分别为Defluviitaleaceae_UCG-011、丁酸球菌属、Prevotellaceae_UCG-004、Candidatus_Saccharimonas、消化球菌属、粪杆菌属、厌氧杆形菌属(Anaerorhabdus_furcosa_group)、聚乙酸菌属(Acetitomaculum)和弯曲杆菌属。在发酵饲料组中(图6D)，共鉴定出10个关键物种，包括2个模块枢纽物种(别样杆菌属和F082)和8个连接物种，分别为胃球菌属、Prevotellaceae_UCG-004、聚乙酸菌属、Lachnospiraceae_XPB1014_group、摩里氏菌属(Moryella)、丝状杆菌属(Fibrobacter)、WCHB1-41和Lachnospiraceae_NK4A136_group。其中，别样杆菌属、F082、Prevotellaceae_UCG-004和聚乙酸菌属在两组中均被识别为关键物种。
3 讨论
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3.1 发酵饲料对跨物种肠道菌群的共性优化
多样性是微生态系统稳定性的直观体现。在现有研究中，发酵饲料对动物肠道微生物α多样性的影响依然存在矛盾性。例如，张孟阳等[6]、Liu等[10]和Li等[15]分别在仔鸡、育肥猪和仔猪的肠道微生物研究中发现发酵饲料导致动物肠道微生物α多样性显著降低；而Tang等[14]和Chen等[24]的研究显示发酵饲料提高了动物肠道菌群的α多样性；另有部分研究表明发酵饲料对动物肠道微生物α多样性无显著影响[21,25,30]。本研究通过Meta分析发现，发酵饲料显著降低了猪、鸡、鹅肠道微生物的α多样性，进一步关联分析表明多样性的降低与动物肠道功能菌群的富集及致病菌的抑制密切相关。这说明α多样性的降低并非意味着肠道微生态系统功能的退化，相反其反映了肠道菌群的生态位优化，促进了肠道菌群向宿主健康增益方向演变。β多样性分析结果表明，发酵饲料并未导致研究动物肠道微生物群落整体结构的显著改变。这与Gu等[19]使用发酵棉籽粕喂食仔猪及Nan等[23]使用发酵葡萄籽粕调控肉鸡肠道菌群的研究结果一致。该结果表明，发酵饲料对动物肠道菌群的生态位优化是在维持群落整体结构的前提下实现的。这种温和的调控模式可能更有利于维持肠道微生态系统的稳定性和功能性，避免了剧烈的群落结构改变可能带来的负面影响。
优势菌属组成反映了肠道菌群的生态功能特征。在发酵饲料组肠道菌群中，瘤胃球菌属、乳杆菌属和粪杆菌属显著富集。已有研究表明，乳杆菌可通过分泌乳酸降低肠道pH值，抑制病原菌定殖并促进短链脂肪酸的合成[36]，而粪杆菌作为核心产丁酸菌，其丰度提升与肠道屏障功能增强及炎症缓解直接相关[37]。瘤胃球菌属是动物消化系统中关键的纤维降解菌属，能够将纤维分解产物转化为乙酸和丁酸[38]。丁酸在动物生理和健康中发挥重要调控作用，具有成为替代抗生素、提升动物健康与生产性能的关键靶点的潜力[39]。本研究发现发酵饲料在不同动物中均能促进产丁酸微生物的协同富集，增强了代谢-免疫协同的肠道微生态网络。在对照组肠道菌群中，弯曲杆菌属、短螺菌属等潜在致病菌丰度较高。弯曲杆菌属等病原菌可通过黏附肠上皮、释放细胞毒素引发腹泻和黏膜损伤[40]，而短螺菌属与肠道螺旋体病等慢性炎症密切相关[41]。BugBase预测进一步显示，发酵饲料组潜在致病性评分显著降低，提示菌群功能向有益方向转化。网络分析揭示了发酵饲料对微生物群落互作网络的优化作用，高连接菌属的增加反映了功能核心的优化[42]。本研究发酵组中的瘤胃球菌属和Fibrobacter替代了对照组中的弯曲杆菌属等致病菌，成为网络中的关键物种。瘤胃球菌属和Fibrobacter能通过调控短链脂肪酸代谢和胆汁酸转化维持网络稳定性[43]。这种网络特征的改变有助于增强微生物间的功能协同以及优化营养物质的利用效率。
3.2 肠道菌群对发酵饲料的宿主特异性响应
在本研究中，不同动物具有各自特征性的优势菌群结构，这反映了宿主-微生物在长期进化过程中形成的共适应关系。猪肠道微生物菌群以产短链脂肪酸菌(梭菌属、乳杆菌属、普雷沃菌属)为主，适应其以淀粉和蛋白质为主的营养需求；牛以纤维素降解菌(普雷沃菌属、理化所菌科RC9群)占优，匹配其植物纤维营养底物；禽类(鸡、鹅)则以拟杆菌属和粪杆菌属为主，反映其独特的消化道生理特征[39]。猪发酵饲料组中芽孢杆菌门的梭菌纲UCG-014群和乳杆菌显著富集，这些菌群通过产生乳酸、细菌素和丁酸，增强了肠道屏障功能并抑制了潜在致病菌的生长，如对照组中显著富集的弯曲杆菌属。牛发酵饲料组中疣微菌门的阿克曼氏菌属和假丁酸弧菌属的富集可以优化反刍动物的纤维素降解和营养代谢[44]。鸡发酵饲料中解黄酮菌属和苏黎世杆菌属的富集，则可以增强碳水化合物代谢和免疫调节功能[45]。
4 结论
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本研究通过整合猪、牛、鸡、鹅的肠道微生物组数据，揭示了发酵饲料调控肠道菌群的跨物种共性规律与宿主特异性机制。在共性层面，发酵饲料通过富集核心功能菌群抑制致病菌，显著降低菌群潜在致病性。在特异性层面，不同动物基于其消化生理特征选择性富集了与宿主营养代谢及免疫调节功能适配的菌群。本研究为开发广谱功能菌株与宿主适配配方相结合的精准发酵饲料技术提供了理论基础。
基金
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  • 国家固态酿造工程技术研究中心资助项目(2024NB04)
  • 四川省大学生创新训练计划(S202410626059)
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2025年第65卷第9期
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doi: 10.13343/j.cnki.wsxb.20250082
  • 接收时间：2025-02-05
  • 首发时间：2026-02-07
  • 出版时间：2025-09-04
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  • 收稿日期：2025-02-05
  • 录用日期：2025-06-27
基金
National Engineering Research Center of Solid-state Brewing Funding Project(2024NB04)
国家固态酿造工程技术研究中心资助项目(2024NB04)
Sichuan Provincial College Student Innovation Training Program(S202410626059)
四川省大学生创新训练计划(S202410626059)
作者信息
    1 四川农业大学 生命科学学院，四川 雅安
    2 重庆大学 生物工程学院，重庆
    3 泸州老窖股份有限公司，四川 泸州
    4 国家固态酿造工程技术研究中心，四川 泸州
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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