Application of Next-Generation Sequencing in the Context of Bacterial and Parasitic Infections

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (15 December 2020) | Viewed by 4321

Special Issue Editors


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Guest Editor
Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
Interests: feed additives; nutritional physiology; microbiology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. College of Life Science and Engineering, Foshan University, Foshan 528231, China
2. Faculty of Science, Kafrelsheikh University, Kafr El-Shaikh, Egypt
Interests: parasitology; immunology; veterinary medicine and next - generation sequencing (MiSeq and HiSeq)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

High-throughput or next-generation sequencing (NGS) is a versatile technology, broadly applicable to bacteria, parasites, and animal hosts. High-throughput technology and bioinformatics unravel the complex landscape and dynamics of transcriptomes at an exceptional level of sensitivity and accuracy, with a dual RNA-seq time course analysis of pathogens and hosts. In recent years, NGS has been applied successfully in a wide range of metagenomic projects that have enormously revolutionized our knowledge of the microbial communities living in and on animal and human bodies. In addition, they can provide new insights into disease transmission, virulence, and antimicrobial resistance. The most common application of amplicon sequencing with NGS technology in the microbiome is 16S rRNA gene sequencing, which is usually employed to assess the bacterial general composition. Metagenome shotgun sequencing provides more intricate information on the microbiome, including gene content and its potential functions. The goal of this Special Issue is to understand the interplay among eukaryotic virome, microbiome, parasites, and animal hosts and their consequences for potential protection. Furthermore, the role of non-coding RNAs in pathogenic infections and their potential as targets for novel treatment paradigms will be covered.

Original papers, communications, and review articles that focus on the latest advances of next-generation sequencing in the context of bacterial and parasitic infections are welcome. Topics include, but are not limited to, the following:

-Disclosing the diversity, composition, and identity of bacterial communities associated with animal hosts in the context of bacterial or parasitic infections;

-Revealing the diversity, composition, and identity of bacterial communities associated with parasites;

-The application of NGS to create transcriptomes for diverse pathogens and tissues in the context of pathogenic infections;

The application of NGS for tackling emerging bacterial and parasitic diseases;-

-Uncovering disease pathogenesis and drug resistance via next-generation sequencing;

-The application of NGS to monitor the spread of antimicrobial resistance and to detect variants of drug-resistant bacteria.

-Exploring the bacteriophage community in the context of bacterial and parasitic infections.

Prof. Dr. Guillermo Tellez-Isaias
Prof. Dr. Saeed Saeed El-Ashram
Guest Editors

Manuscript Submission Information

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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.

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Keywords

  • High-throughput/next-generation sequencing (NGS)
  • bacteria
  • parasites
  • animal hosts
  • eukaryotic virome
  • bioinformatics
  • pathogens and hosts
  • pathogenic infections
  • bacterial and parasitic infections
  • disease transmission
  • virulence
  • antimicrobial resistance
  • 16S rRNA gene sequencing
  • Metagenome shotgun sequencing

Published Papers (1 paper)

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Research

20 pages, 3744 KiB  
Article
Effect of Dietary Fiber Sources on In-Vitro Fermentation and Microbiota in Monogastrics
by Asavela Ngalavu, Hailong Jiang, Saeed El-Ashram, Guillermo Tellez-Isaias, Mohammed Hamdy Farouk, Pakama Siphelele Nyingwa, Adams Seidu and Thobela Louis Tyasi
Animals 2020, 10(4), 674; https://doi.org/10.3390/ani10040674 - 13 Apr 2020
Cited by 5 | Viewed by 3322
Abstract
Feed fiber composition is usually considered as one of the factors that have an impact on digestive tract microbiota composition. The investigations on the level of fermentation and in-vitro digestibility of different fibers are not well understood. The aim of the current study [...] Read more.
Feed fiber composition is usually considered as one of the factors that have an impact on digestive tract microbiota composition. The investigations on the level of fermentation and in-vitro digestibility of different fibers are not well understood. The aim of the current study is to determine the effect of different fiber sources on intestinal nutrient digestibility, hindgut fermentation, and microbial community composition under in vitro conditions using pigs’ hindgut as a model. The experimental treatment diets contained alfalfa hay, cornstalk, and rice straw. Cornstalk treatment displayed higher digestibility compared to alfalfa hay and rice straw; similar results were observed with in-vitro digestibility using intestinal digesta. Firmicutes were the most abundant phyla (Firmicutes = 89.2%), and Lactobacillus were the prominent genera (75.2%) in response to alfalfa compared to rice straw and cornstalk treatments. In simulated in-vitro digestion, corn stalk fiber improved dry matter digestibility; rice straw fiber improved volatile fatty acid content and fermentation efficiency. Alfalfa fiber improved the thickness of deposited Firmicutes and Lactobacillus. Full article
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