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      Ruminal microbiota-host crosstalks promote ruminal epithelial development in neonatal lambs with alfalfa hay introduction

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      1 , 2 , 3 , 1 , 2 , 4 , 2 , 3 ,
      mSystems
      American Society for Microbiology
      sucking lambs, alfalfa hay, rumen development, microbial community, epithelial function

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          ABSTRACT

          Ruminal microbiota is gradually established after birth, while microbiota maturation could be highly diverse because of varied solid dietary accessibility. However, how the ruminal microbiota accreted from postnatal hay diets alters rumen epithelial development, and how this affects animal health remains largely unknown. Here, neonatal lambs were introduced to starchy corn-soybean starter or corn-soybean starter + alfalfa hay (AH) to investigate the influences of early life ruminal microbiome on rumen epithelial development using integrated 16s rRNA sequencing-metagenome-transcriptome approaches. The results showed that AH introduction elevated average daily weight gain, rumen weight and volume, rumen epithelial papillae length, and rumen muscle layer thickness. Meanwhile, the relative abundance of fibrolytic bacteria ( Christensenellaceae R-7 group, Prevotellaceae UCG-001, and Succinivibrio), acetate producer ( Acetitomaculum and Mitsuokella), and propionate producer Succiniclasticum was increased in the rumen content by AH supplementation ( P < 0.05). Moreover, AH introduction decreased the relative abundance of total CAZymes, CBM, and GH and increased the abundance of KO genes related to volatile fatty acid (VFA) generation in the rumen content. AH lambs had a higher relative abundance of Succiniclasticum, Megasphaera, Succinivibrio, and Suttonella ( P < 0.05), while a lower relative abundance of Cloacibacillus, Desulfovibrio, Dialister, Intestinimonas, Parabacteroides, and Pseudoscardovia ( P < 0.05) in the rumen epithelial samples. Furthermore, these alterations in ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation. In summary, AH introduction benefited ruminal fiber degradation and VFA generation bacteria colonization and promoted ruminal epithelial development. These findings provide new insights into ruminal microbial–host interactions in the early life.

          IMPORTANCE

          While it is established that a fiber-rich diet promotes rumen development in lambs, further research is needed to investigate the precise response of rumen microbiota and epithelium to high-quality alfalfa hay. Here, we observed that the inclusion of alfalfa hay led to a discernible alteration in the developmental trajectory of the rumen. Notably, there was a favorable shift in the rumen's volume, morphology, and the development of rumen papillae. Furthermore, ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation, collectively provide compelling evidence supporting the capacity of alfalfa hay to enhance rumen development and health through ruminal micrbiota-host crosstalks. Our findings elucidate the functional response of the rumen to alfalfa hay introduction, providing new insights into strategies for promoting healthy development of the rumen in young ruminants.

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          Most cited references72

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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              Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

              DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
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                Author and article information

                Contributors
                Role: Writing – original draftRole: Writing – review and editing
                Role: Data curationRole: Writing – original draftRole: Writing – review and editing
                Role: Formal analysisRole: InvestigationRole: Project administration
                Role: Data curationRole: Formal analysisRole: Writing – original draftRole: Writing – review and editing
                Role: Editor
                Journal
                mSystems
                mSystems
                msystems
                mSystems
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2379-5077
                February 2024
                05 January 2024
                05 January 2024
                : 9
                : 2
                : e01034-23
                Affiliations
                [1 ]College of Animal Science and Food Engineering, Jinling Institute of Technology; , Nanjing, China
                [2 ]Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University; , Nanjing, China
                [3 ]National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University; , Nanjing, China
                [4 ]College of Food Science and Technology, Nanjing Agricultural University; , Nanjing, China
                State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences; , Beijing, China
                Author notes
                Address correspondence to Junhua Liu, liujunhua0011@ 123456163.com

                Gaorui Bian and Shiqiang Yu contributed equally to this article. Author order was determined both alphabetically and in order of increasing seniority.

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0002-1381-7912
                https://orcid.org/0000-0002-1028-5586
                Article
                01034-23 msystems.01034-23
                10.1128/msystems.01034-23
                10878101
                38179946
                bd87496d-8893-45c3-9630-921d0d0c4981
                Copyright © 2024 Bian et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 25 September 2023
                : 23 October 2023
                Page count
                supplementary-material: 1, authors: 5, Figures: 6, Tables: 2, References: 73, Pages: 18, Words: 9905
                Funding
                Funded by: MOST | National Key Research and Development Program of China (NKPs);
                Award ID: 2021YFF1000703
                Award Recipient :
                Funded by: Resrarch Fund of Jinling Inetitute of Techology;
                Award ID: 040521200117
                Award Recipient :
                Categories
                Research Article
                host-microbial-interactions, Host-Microbial Interactions
                Custom metadata
                February 2024

                sucking lambs,alfalfa hay,rumen development,microbial community,epithelial function

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