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Animals
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Food Animal Microbiomes: Food Production, Microbes, and One Health
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Food Animal Microbiomes: Food Production, Microbes, and One Health

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 19852

Special Issue Editor

Prof. Erika Ganda

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Guest Editor
Pennsylvania State University, University Park, PA, USA

Special Issue Information

Dear Colleagues,

The effects of the microbiota in host physiological aspects, such as body weight and composition, have been studied for over 10 years in mice and humans. However, the field of microbiome research in food production animals is just starting to unleash its potential. To date, many studies have identified associations between the microbiome, productivity, and management practices in various food animal species; yet, the specific organisms and metabolic pathways involved remain to be determined. Food production is intensively dependent on the microbiome, and in the face of the predicted global population growth, measures must be taken to meet the needs of forecasted animal protein production.

Medically important antibiotics are highly regulated in regards to their use in feed or water of food-producing animals, which calls for alternative approaches to obtain efficient animal production. The growing body of evidence points to the potential of modifying the microbiome of various species to improve production performance. Recently published work has identified that specific feed supplementation (nutraceuticals, prebiotics, probiotics, tailored symbiotics) improves production performance in various food-producing species; however, the specific organisms and mechanisms involved in this improvement remain to be described. Likewise, the gut microbiota composition has been shown to differ between high- and low-feed-conversion animals, and sub-lethal doses of antibiotics have been demonstrated to selectively enrich for bacteria associated with improved gut health. Achieving growth promotion and feed conversion benefits without the use of antibiotics would be advantageous for the agricultural industry and public health.

With the goal to publish research that will have an impact on improving animal health, productivity, and food safety, we invite the submission of original manuscripts and review articles that address the many areas of research involved in safe production of animal-based foods. Topics of interest include the following:

  • Mechanisms responsible for beneficial effects observed in various feeding strategies;
  • Precision feeding based on microbiomes;
  • Mitigating antimicrobial resistance in the food supply;
  • Best practices for the development of tailored probiotics;
  • Effect of nutraceuticals, prebiotics, and probiotics in food animal’s health and productivity.

Prof. Erika Ganda
Guest Editor

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

  • microbiomes
  • livestock
  • poultry
  • cattle
  • swine
  • probiotics
  • precision feeding
  • antimicrobial resistance
  • food supply chain
  • symbiotics
  • nutraceuticals

Published Papers (5 papers)

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Research

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16 pages, 1283 KiB  
Article
Relationships among Indicators of Metabolism, Mammary Health and the Microbiomes of Periparturient Holstein Cows
by Daniela C. Tardón, Christian Hoffmann, Fernanda C. R. Santos, Nathalia Decaris, Filipe A. Pinheiro, Luciano L. Queiroz, David J. Hurley and Viviani Gomes
Animals 2022, 12(1), 3; https://0-doi-org.brum.beds.ac.uk/10.3390/ani12010003 - 21 Dec 2021
Cited by 3 | Viewed by 3641
Abstract
During the period called “transition”, from the ceasing of milk production to the reestablishment of full milk production, it is postulated that the microbiota of cows undergo changes in composition driven by the fluxes in systemic energetics and that these changes appear to [...] Read more.
During the period called “transition”, from the ceasing of milk production to the reestablishment of full milk production, it is postulated that the microbiota of cows undergo changes in composition driven by the fluxes in systemic energetics and that these changes appear to impact the health of cows. The primary objective of this study was to document the make-up of the microbiota in the mammary gland compared with those in the vagina and in feces in an attempt to determine any correlations between the composition of the microbiota, the impact of blood indicators of energetic metabolites and the health of the mammary gland at the time of calving. Samples were collected from 20 Holstein dairy cows immediately following calving to assess their general health and measure the microbiomes associated with each cow using 16S rRNA sequencing. The results indicated that the microbiomes found within each maternal niche were different. A set of significant negative associations between the blood energetic biomarkers (NEFAs, BHB, triglycerides and cholesterol) and the taxa Pseudomonas, Christensenellaceae and Methanobrevibacter were observed in this study. In contrast, Escherichia and Romboutsia were positively correlated with the same energetic metabolites. Therefore, it was concluded that there appears to be a set of relationships between the microorganisms that colonize several niches of cows and the sufficiency of systemic energy metabolism. Furthermore, both the microbiome and energy dynamics impact the health of the mammary gland of the host. Full article
(This article belongs to the Special Issue Food Animal Microbiomes: Food Production, Microbes, and One Health)
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10 pages, 3331 KiB  
Article
Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis
by Mohamed Zeineldin, Ameer Megahed, Benjamin Blair, Brian Aldridge and James Lowe
Animals 2021, 11(6), 1825; https://0-doi-org.brum.beds.ac.uk/10.3390/ani11061825 - 18 Jun 2021
Cited by 3 | Viewed by 2078
Abstract
The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on [...] Read more.
The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production. Full article
(This article belongs to the Special Issue Food Animal Microbiomes: Food Production, Microbes, and One Health)
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12 pages, 1584 KiB  
Article
Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs
by Emily Van Syoc, Natália Carrillo Gaeta and Erika Ganda
Animals 2021, 11(5), 1372; https://0-doi-org.brum.beds.ac.uk/10.3390/ani11051372 - 12 May 2021
Cited by 1 | Viewed by 3081
Abstract
As the applications of microbiome science in agriculture expand, laboratory methods should be constantly evaluated to ensure optimization and reliability of downstream results. Most animal microbiome research uses fecal samples or rectal swabs for profiling the gut bacterial community; however, in birds, this [...] Read more.
As the applications of microbiome science in agriculture expand, laboratory methods should be constantly evaluated to ensure optimization and reliability of downstream results. Most animal microbiome research uses fecal samples or rectal swabs for profiling the gut bacterial community; however, in birds, this is difficult given the unique anatomy of the cloaca where the fecal, urinary, and reproductive tracts converge into one orifice. Therefore, avian gut microbiomes are usually sampled from cloacal swabs, creating a need to evaluate sample preparation methods to optimize 16S sequencing. We compared four different DNA extraction methods from two commercially available kits on cloacal swabs from 10 adult commercial laying hens and included mock communities and negative controls, which were then subjected to 16S rRNA amplicon sequencing. Extracted DNA yield and quality, diversity analyses, and contaminants were assessed. Differences in DNA quality and quantity were observed, and all methods needed further purification for optimal sequencing, suggesting contaminants due to cloacal contents, method reagents, and/or environmental factors. However, no differences were observed in alpha or beta diversity between methods. Importantly, multiple bacterial contaminants were detected in each mock community and negative control, indicating the prevalence of laboratory and handling contamination as well as method-specific reagent contamination. We found that although the extraction methods resulted in different extraction quality and yield, overall sequencing results were not affected, and we did not identify any method that would be an inappropriate choice in extracting DNA from cloacal swabs for 16S rRNA sequencing. Overall, our results highlight the need for careful consideration of positive and negative controls in addition to DNA isolation method and lend guidance to future microbiome research in poultry. Full article
(This article belongs to the Special Issue Food Animal Microbiomes: Food Production, Microbes, and One Health)
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18 pages, 1660 KiB  
Article
The Influence of Essential Oils on Gut Microbial Profiles in Pigs
by Modestas Ruzauskas, Elena Bartkiene, Arunas Stankevicius, Jurga Bernatoniene, Daiva Zadeike, Vita Lele, Vytaute Starkute, Paulina Zavistanaviciute, Juozas Grigas, Egle Zokaityte, Arnoldas Pautienius, Grazina Juodeikiene and Valdas Jakstas
Animals 2020, 10(10), 1734; https://0-doi-org.brum.beds.ac.uk/10.3390/ani10101734 - 24 Sep 2020
Cited by 17 | Viewed by 3768
Abstract
In recent years, the intake of ultra-processed foods has increased dramatically worldwide. Missing natural foods in the diet raise the need of biologically active food components that could compensate for this deficiency and help maintain proper immune status. This study used pigs as [...] Read more.
In recent years, the intake of ultra-processed foods has increased dramatically worldwide. Missing natural foods in the diet raise the need of biologically active food components that could compensate for this deficiency and help maintain proper immune status. This study used pigs as an animal model for the assessment of the impact of consumption of Origanum vulgare plant extract combined with Mentha piperita and Thymus vulgaris essential oils on microbial profile in intestines. A single group of weaned pigs received basal diet, while the other group basal diet supplemented with plant extract and two essential oils in the form of bilayer tablets prepared using “liquid/solid” phase technology. Metagenomic sequencing was performed with the aim to investigate changes of microbial communities in ileum, caecum, and colon. The results demonstrated that the combination of essential oils was non cytotoxic, and had a positive effect on the microbial composition in the large intestine of pigs due to significant increase in the number of probiotic bacteria. The amount of Lactobacillus was 2.5 times and Bifidobacterium 1.9 times higher in the animal group fed with supplement. The combination, however, had some negative impact on the variety of minor species in the distal part of the ileum. Additional studies need to be performed to obtain knowledge on how combinations of essential oils can change bacterial variety in the proximal part of the gastrointestinal tract. Full article
(This article belongs to the Special Issue Food Animal Microbiomes: Food Production, Microbes, and One Health)
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Review

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55 pages, 863 KiB  
Review
A Review of the Effects and Production of Spore-Forming Probiotics for Poultry
by Igor V. Popov, Ammar Algburi, Evgeniya V. Prazdnova, Maria S. Mazanko, Vladimir Elisashvili, Anzhelica B. Bren, Vladimir A. Chistyakov, Elizaveta V. Tkacheva, Vladimir I. Trukhachev, Irina M. Donnik, Yuri A. Ivanov, Dmitry Rudoy, Alexey M. Ermakov, Richard M. Weeks and Michael L. Chikindas
Animals 2021, 11(7), 1941; https://0-doi-org.brum.beds.ac.uk/10.3390/ani11071941 - 29 Jun 2021
Cited by 25 | Viewed by 5974
Abstract
One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, [...] Read more.
One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, which is a concern not only in animals, but for humans as well. One of the promising ways to overcome this challenge is found in probiotics due to their wide range of features and mechanisms of action for health promotion. Moreover, spore-forming probiotics are suitable for use in the poultry industry because of their unique ability, encapsulation, granting them protection from the harshest conditions and resulting in improved availability for hosts’ organisms. This review summarizes the information on gastrointestinal tract microbiota of poultry and their interaction with commensal and probiotic spore-forming bacteria. One of the most important topics of this review is the absence of uniformity in spore-forming probiotic trials in poultry. In our opinion, this problem can be solved by the creation of standards and checklists for these kinds of trials such as those used for pre-clinical and clinical trials in human medicine. Last but not least, this review covers problems and challenges related to spore-forming probiotic manufacturing. Full article
(This article belongs to the Special Issue Food Animal Microbiomes: Food Production, Microbes, and One Health)
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