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Animals
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Microbiome Genomics in Livestock Production
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Microbiome Genomics in Livestock Production

A special issue of Animals (ISSN 2076-2615).

Deadline for manuscript submissions: closed (16 January 2024) | Viewed by 3384

Special Issue Editors

Dr. Udaya DeSilva

E-Mail Website
Guest Editor
Department of Animal Science, Oklahoma State University, Stillwater, OK, USA
Interests: metagenomics of the female reproductive tract; gastrointestinal tract microbiome; rumen microbiome; viromes of reproductive and gastrointestinal tracts of domestic animals; animal adaptation to drought, functional genomics of adipogenesis
Dr. Jenny L. Sones

E-Mail Website
Guest Editor
Equine Reproduction Laboratory, Colorado State University, Fort Collins, CO 80521, USA
Interests: comparative pregnancy physiology; preeclampsia and fetal growth restriction; equine placentitis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The advent of ‘omics technologies had revolutionized the study of complex interactions between the host and its microbiome (bacteria, archaea, fungi, protozoa, and viruses) and the role of the microbiome in animal health, disease and productivity. A field that was dominated by 16S rDNA amplicon sequencing has progressed into whole genome sequencing of environments, metagenome wide association studies (MWAS), genome wide association studies (GWAS) of interplay between host genetic variation and its microbiome to meta transcriptomics. Microbial genomics in livestock animals is still in its infancy but, recent publication of several ground-breaking studies describing interaction of host genomics with gut microbiomes, genomics of drug resistance, impact of microbe-pathogen interactions, establishment and characterization of commensal viromes in many livestock species and genomics approaches to study phage therapy etc. proves that microbial genomics has become a subject of immense interest in livestock species.

This research topic focuses on metagenomic sequencing and analyses, bacterial genomics-based pathogen surveillance, genome-based study of bacterial, fungal, protozoal and viral communities, meta-transcriptomics of microbiome communities, environmental impact of livestock microbial communities, etc. and their role in health, disease, and productivity of all major and minor livestock species.

Dr. Udaya DeSilva
Dr. Jenny L. Sones
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

 

Keywords

  • metagenomics
  • metatranscriptomics
  • microbiome
  • virome
  • livestock
  • DNA-Seq
  • RNA-Seq
  • miRNA-Seq

Published Papers (2 papers)

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Research

14 pages, 3862 KiB  
Article
Metagenetic Analysis of the Pregnant Microbiome in Horses
by Kalie F. Beckers, Viviane C. L. Gomes, Kassandra R. Crissman, Chin-Chi Liu, Christopher J. Schulz, Gary W. Childers and Jenny L. Sones
Animals 2023, 13(12), 1999; https://doi.org/10.3390/ani13121999 - 15 Jun 2023
Cited by 2 | Viewed by 1467
Abstract
Placentitis is the leading cause of infectious abortion in the horse. Additionally, it can result in weak and/or growth restricted offspring. While the etiology of ascending placentitis is well described in mares, less is known regarding the pathogenesis of other types, such as [...] Read more.
Placentitis is the leading cause of infectious abortion in the horse. Additionally, it can result in weak and/or growth restricted offspring. While the etiology of ascending placentitis is well described in mares, less is known regarding the pathogenesis of other types, such as nocardioform placentitis. This study aims to identify the microbial communities in different body sites of the pregnant mare in early gestation to establish a core microbiome that may be perturbed in pathologic pregnancies such as placentitis. We hypothesize that the equine placenta harbors a distinct resident microbiome in early pregnancy when characterized by metagenetics and that there will be a disparity in bacterial communities from the oral, vaginal, and fecal microbiome. Samples were collected from the oral cavity, vagina, anus, and the allantoic portion of the allantochorion (“placenta”) from five pregnant mares between 96 and 120 days of gestation. The V4 region of the 16S rRNA gene was amplified for Illumina MiSeq sequencing to examine core bacterial communities present in the different body sites. Microbial community composition of the pregnant ponies by body site was significantly different (Bray–Curtis dissimilarity). The placenta was significantly different from the feces, oral cavity, and vagina. Alpha diversity measuring the Shannon diversity matrix was significant, with the body sites being a compounding variable, meaning there was a difference in richness and evenness in the different microbial communities. Feces had the greatest alpha diversity, while the oral cavity and placenta similarly had the least. In conclusion, metagenetics did reveal distinct community differences in the oral, fecal, vaginal, and placenta cavities of the horse. The equine placenta does show similarities in its microbial communities to the oral cavity. Further research needs to be completed to investigate how bacteria may be translocated to the placenta from these other body sites and how they contribute to the development of placentitis. Full article
(This article belongs to the Special Issue Microbiome Genomics in Livestock Production)
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14 pages, 1544 KiB  
Article
Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma
by Hannah B. Gafen, Chin-Chi Liu, Nikole E. Ineck, Clare M. Scully, Melanie A. Mironovich, Lauren Guarneri, Christopher M. Taylor, Meng Luo, Marina L. Leis, Erin M. Scott, Renee T. Carter and Andrew C. Lewin
Animals 2023, 13(12), 1976; https://doi.org/10.3390/ani13121976 - 13 Jun 2023
Cited by 3 | Viewed by 1233
Abstract
The ocular surface microbiome is altered in certain disease states. The aim of this study was to characterize the bovine bacterial ocular surface microbiome (BBOSM) in the context of ocular squamous cell carcinoma (OSCC). The conjunctiva of normal (n = 28) and [...] Read more.
The ocular surface microbiome is altered in certain disease states. The aim of this study was to characterize the bovine bacterial ocular surface microbiome (BBOSM) in the context of ocular squamous cell carcinoma (OSCC). The conjunctiva of normal (n = 28) and OSCC (n = 10) eyes of cows aged 2 to 13 years from two farms in Louisiana and Wyoming were sampled using individual sterile swabs. DNA extraction followed by 16S ribosomal ribonucleic acid (rRNA) gene sequencing and real-time polymerase chain reaction (RT-PCR) were performed to, respectively, assess the relative and absolute BBOSM. Discriminant analysis (DA) was performed using RT-PCR data, and relative abundance analysis was performed using 16S rRNA gene sequencing data. The 11 most abundant phyla in both normal and OSCC-affected cows were identified using 16S rRNA gene sequencing analysis. The relative abundance of Euryarchaeota was found to be significantly lower (p = 0.0372) in OSCC eyes compared to normal eyes. Relative abundance differences within and between geographic locations were also identified. Quadratic DA categorized samples as OSCC or normal with 100% sensitivity and 83.3–100% specificity. Relative abundance analysis identified relative BBOSM phylum alterations in OSCC. Quadratic DA can be used to accurately categorize BBOSM from normal and OSCC ocular surface samples. Full article
(This article belongs to the Special Issue Microbiome Genomics in Livestock Production)
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