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Pathogens
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Modulation of Gut Microbiota & Microbiome in Pigs
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Modulation of Gut Microbiota & Microbiome in Pigs

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 18825

Special Issue Editors

Prof. Dr. Ming Z. Fan

E-Mail Website
Guest Editor
Department of Animal Biosciences (ABSc), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
Interests: gastrointestinal physiology; nutrition and metabolism; gut microbiota and microbiome; gut dysbiosis; antimicrobial resistance; metabolic endotoxemia; systemic inflammation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Sung Woo Kim

E-Mail Website
Guest Editor
Department of Animal Science, North Carolina State University, 116 Polk Hall, Campus Box 7621, Raleigh, NC 27695, USA
Interests: monogastric nutrition; digestive physiology; intestinal health; maternal and perinatal nutrition; swine production
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I am pleased to have this opportunity to guest-edit a Special Issue on “Gut Microbiota and Microbiome in Pigs” with implications for controlling porcine gut pathogen and improving porcine gut health, swine nutrition, and efficiency of pork production and for mitigating major negative impacts of intensive pork production on environment.

While next-generation sequencing (NGS) platforms have been widely used to unravel porcine gut microbial diversity and microbial genes primarily at fecal levels as affected by dietary, therapeutic, and physiological factors, new progress needs to be made to establish causal relationships between functional outcomes and gut microbial species or their genes along the small and large intestinal longitudinal axis. The application of NGS platforms to reveal how changes in porcine gut virome are linked to host health and functions is also important.

This Special Issue invites focused reviews and original research in i) looking at how dietary such as exogenous enzymes, prebiotics and probiotics, therapeutics such as antibiotics and pharmacological levels of zinc oxide, and physiological factors such as cold or thermal stress affect porcine gut microbial diversity; ii) identifying specific bacterial species and viruses causing health and productivity concerns, such as weaning-associated gut dysbiosis, diarrhea, and growth lag; and iii) establishing possible causal relationships between functional outcomes, such as fiber digestion, fermentation of amino acids and biogenesis of major volatile odor compounds and antimicrobial resistance, and abundances of identified gut microbes at phylum or species level and rate-limiting microbial pathway genes in the porcine gut.

Prof. Dr. Ming Z. Fan
Prof. Dr. Sung Woo Kim
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. Pathogens is an international peer-reviewed open access monthly 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 2200 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

  • Antibiotics & antimicrobials
  • Diets, ingredients and nutrient composition
  • Prebiotics
  • Probiotics
  • Exogenous enzymes
  • Antimicrobial resistance genes
  • Partial and whole 16S rRNA gene sequencing
  • Shotgun metagenomic sequencing and bioinformatics
  • Microbial gene-centric cataloguing and annotation
  • Pathogenic bacteria and viruses
  • Bacterial fibre degradation pathway rate-limiting enzyme genes
  • Bacterial amino acid degradation pathway rate-limiting enzyme genes
  • Bacterial starch and sugar degradation pathway rate-limiting enzyme gene

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Published Papers (6 papers)

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Editorial

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5 pages, 198 KiB  
Editorial
Modulation of Porcine Gut Microbiota and Microbiome: Hologenomic, Dietary, and Endogenous Factors
by Ming Z. Fan and Sung Woo Kim
Pathogens 2024, 13(3), 225; https://doi.org/10.3390/pathogens13030225 - 5 Mar 2024
Cited by 1 | Viewed by 1439
Abstract
Global pig production contributes to about 35% of the world’s meat production and consumption [...] Full article
(This article belongs to the Special Issue Modulation of Gut Microbiota & Microbiome in Pigs)

Research

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11 pages, 1028 KiB  
Article
A Comparative Analysis of the Fecal Bacterial Communities of Light and Heavy Finishing Barrows Raised in a Commercial Swine Production Environment
by Emily C. Fowler, Ryan S. Samuel and Benoit St-Pierre
Pathogens 2023, 12(5), 738; https://doi.org/10.3390/pathogens12050738 - 20 May 2023
Cited by 3 | Viewed by 1835
Abstract
For commercial swine producers, the natural variation in body weight amongst pigs in a herd presents a challenge in meeting the standards of meat processors who incentivize target carcass weights by offering more favorable purchase prices. Body weight variation in a swine herd [...] Read more.
For commercial swine producers, the natural variation in body weight amongst pigs in a herd presents a challenge in meeting the standards of meat processors who incentivize target carcass weights by offering more favorable purchase prices. Body weight variation in a swine herd is evident as early as birth, and it is typically maintained throughout the entire production cycle. Amongst the various factors that can affect growth performance, the gut microbiome has emerged as an important factor that can affect efficiency, as it contributes to vital functions such as providing assimilable nutrients from feed ingredients that are inedible to the host, as well as resistance to infection by a pathogen. In this context, the objective of the study described in this report was to compare the fecal microbiomes of light and heavy barrows (castrated male finishing pigs) that were part of the same research herd that was raised under commercial conditions. Using high-throughput sequencing of amplicons generated from the V1-V3 regions of the 16S rRNA gene, two abundant candidate bacterial species identified as operational taxonomic units (OTUs), Ssd-1085 and Ssd-1144, were found to be in higher abundance in the light barrows group. Ssd-1085 was predicted to be a potential strain of Clostridium jeddahitimonense, a bacterial species capable of utilizing tagatose, a monosaccharide known to act as a prebiotic that can enhance the proliferation of beneficial microorganisms while inhibiting the growth of bacterial pathogens. OTU Ssd-1144 was identified as a candidate strain of C. beijerinckii, which would be expected to function as a starch utilizing symbiont in the swine gut. While it remains to be determined why putative strains of these beneficial bacterial species would be in higher abundance in lower weight pigs, their overall high levels in finishing pigs could be the result of including ingredients such as corn and soybean-based products in swine diets. Another contribution from this study was the determination that these two OTUs, along with five others that were also abundant in the fecal bacterial communities of the barrows that were analyzed, had been previously identified in weaned pigs, suggesting that these OTUs can become established as early as the nursery phase. Full article
(This article belongs to the Special Issue Modulation of Gut Microbiota & Microbiome in Pigs)
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28 pages, 2810 KiB  
Article
Deglycosylation Differentially Regulates Weaned Porcine Gut Alkaline Phosphatase Isoform Functionality along the Longitudinal Axis
by Xindi Yin, Weijun Wang, Stephen Y. K. Seah, Yoshinori Mine and Ming Z. Fan
Pathogens 2023, 12(3), 407; https://doi.org/10.3390/pathogens12030407 - 3 Mar 2023
Cited by 2 | Viewed by 2029
Abstract
Gut alkaline phosphatases (AP) dephosphorylate the lipid moiety of endotoxin and other pathogen-associated-molecular patterns members, thus maintaining gut eubiosis and preventing metabolic endotoxemia. Early weaned pigs experience gut dysbiosis, enteric diseases and growth retardation in association with decreased intestinal AP functionality. However, the [...] Read more.
Gut alkaline phosphatases (AP) dephosphorylate the lipid moiety of endotoxin and other pathogen-associated-molecular patterns members, thus maintaining gut eubiosis and preventing metabolic endotoxemia. Early weaned pigs experience gut dysbiosis, enteric diseases and growth retardation in association with decreased intestinal AP functionality. However, the role of glycosylation in modulation of the weaned porcine gut AP functionality is unclear. Herein three different research approaches were taken to investigate how deglycosylation affected weaned porcine gut AP activity kinetics. In the first approach, weaned porcine jejunal AP isoform (IAP) was fractionated by the fast protein-liquid chromatography and purified IAP fractions were kinetically characterized to be the higher-affinity and lower-capacity glycosylated mature IAP (p < 0.05) in comparison with the lower-affinity and higher-capacity non-glycosylated pre-mature IAP. The second approach enzyme activity kinetic analyses showed that N-deglycosylation of AP by the peptide N-glycosidase-F enzyme reduced (p < 0.05) the IAP maximal activity in the jejunum and ileum and decreased AP affinity (p < 0.05) in the large intestine. In the third approach, the porcine IAP isoform-X1 (IAPX1) gene was overexpressed in the prokaryotic ClearColiBL21 (DE3) cell and the recombinant porcine IAPX1 was associated with reduced (p < 0.05) enzyme affinity and maximal enzyme activity. Therefore, levels of glycosylation can modulate plasticity of weaned porcine gut AP functionality towards maintaining gut microbiome and the whole-body physiological status. Full article
(This article belongs to the Special Issue Modulation of Gut Microbiota & Microbiome in Pigs)
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20 pages, 1630 KiB  
Article
Significance of Mucosa-Associated Microbiota and Its Impacts on Intestinal Health of Pigs Challenged with F18+ E. coli
by Marcos Elias Duarte and Sung Woo Kim
Pathogens 2022, 11(5), 589; https://doi.org/10.3390/pathogens11050589 - 17 May 2022
Cited by 19 | Viewed by 4370
Abstract
The objective of this study was to evaluate the significance of jejunal mucosa-associated microbiota and its impacts on the intestinal health of pigs challenged with F18+ Escherichia coli. Forty-four newly-weaned pigs were allotted to two treatments in a randomized complete [...] Read more.
The objective of this study was to evaluate the significance of jejunal mucosa-associated microbiota and its impacts on the intestinal health of pigs challenged with F18+ Escherichia coli. Forty-four newly-weaned pigs were allotted to two treatments in a randomized complete block design with sex as blocks. Pigs were fed common diets for 28 d. At d 7 post-weaning, pigs were orally inoculated with saline solution or F18+ E. coli. At d 21 post-challenge, feces and blood were collected and pigs were euthanized to collect jejunal tissue to evaluate microbiota and intestinal health parameters. The relative abundance of Firmicutes and Bacteroidetes was lower (p < 0.05) in jejunal mucosa than in feces, whereas Proteobacteria was greater (p < 0.05) in jejunal mucosa. F18+ E. coli increased (p < 0.05) protein carbonyl, Helicobacteraceae, Pseudomonadaceae, Xanthomonadaceae, and Peptostreptococcaceae and reduced (p < 0.05) villus height, Enterobacteriaceae, Campylobacteraceae, Brachyspiraceae, and Caulobacteraceae in jejunal mucosa, whereas it reduced (p < 0.05) Spirochaetaceae and Oscillospiraceae in feces. Collectively, jejunal mucosa-associated microbiota differed from those in feces. Compared with fecal microbiota, the change of mucosa-associated microbiota by F18+ E. coli was more prominent, and it was mainly correlated with increased protein carbonyl and reduced villus height in jejunal mucosa impairing the intestinal health of nursery pigs. Full article
(This article belongs to the Special Issue Modulation of Gut Microbiota & Microbiome in Pigs)
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10 pages, 1225 KiB  
Article
Effects of Partially Hydrolyzed Guar Gum Supplementation on the Fecal Microbiotas of Piglets
by Ryo Inoue, Hikari Otabi, Taiga Yamashita, Naoya Takizawa, Toshinobu Kido, Akira Sugiyama, Makoto Ozeki, Aya Abe and Takamitsu Tsukahara
Pathogens 2021, 10(11), 1420; https://doi.org/10.3390/pathogens10111420 - 1 Nov 2021
Cited by 3 | Viewed by 3130
Abstract
Probiotics and prebiotics have become viable alternatives of growth-promoting antimicrobials in animal production. Here, we tested partially hydrolyzed guar gum (PHGG) as a possible prebiotic for piglets in the commercial farm. Five hundred and ninety-four piglets were used for the experiments, with 293 [...] Read more.
Probiotics and prebiotics have become viable alternatives of growth-promoting antimicrobials in animal production. Here, we tested partially hydrolyzed guar gum (PHGG) as a possible prebiotic for piglets in the commercial farm. Five hundred and ninety-four piglets were used for the experiments, with 293 given a normal pig feed (control), while the rest the feed plus 0.06% (w/w) of PHGG (PHGG). One and three months post-PHGG supplementation, fecal samples were collected from randomly selected 20 piglets in each group and analyzed for microbiota and organic acid concentrations. Notably, the abundance of Streptococcus, and unclassified Ruminococcaceae were lower (p < 0.05) in PHGG than in control, one-month post-supplementation. Lactobacillus and Prevotella were higher (p < 0.05), while Streptococcus was lower (p < 0.05), in PHGG than in control, three months post-supplementation. The concentrations of acetate, propionate, and butyrate were greater in PHGG than in control, three months post-supplementation. Finally, PHGG grew faster and had fewer deaths until slaughter time (p < 0.05), than control. We concluded that PHGG not only was an effective prebiotic to alter gut microbiota of weanling piglets but also can possibly promote body weight accretion and health. Full article
(This article belongs to the Special Issue Modulation of Gut Microbiota & Microbiome in Pigs)
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Review

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36 pages, 2756 KiB  
Review
Polyphenols: Bioavailability, Microbiome Interactions and Cellular Effects on Health in Humans and Animals
by Michael B. Scott, Amy K. Styring and James S. O. McCullagh
Pathogens 2022, 11(7), 770; https://doi.org/10.3390/pathogens11070770 - 5 Jul 2022
Cited by 28 | Viewed by 4454
Abstract
Polyphenolic compounds have a variety of functions in plants including protecting them from a range of abiotic and biotic stresses such as pathogenic infections, ionising radiation and as signalling molecules. They are common constituents of human and animal diets, undergoing extensive metabolism by [...] Read more.
Polyphenolic compounds have a variety of functions in plants including protecting them from a range of abiotic and biotic stresses such as pathogenic infections, ionising radiation and as signalling molecules. They are common constituents of human and animal diets, undergoing extensive metabolism by gut microbiota in many cases prior to entering circulation. They are linked to a range of positive health effects, including anti-oxidant, anti-inflammatory, antibiotic and disease-specific activities but the relationships between polyphenol bio-transformation products and their interactions in vivo are less well understood. Here we review the state of knowledge in this area, specifically what happens to dietary polyphenols after ingestion and how this is linked to health effects in humans and animals; paying particular attention to farm animals and pigs. We focus on the chemical transformation of polyphenols after ingestion, through microbial transformation, conjugation, absorption, entry into circulation and uptake by cells and tissues, focusing on recent findings in relation to bone. We review what is known about how these processes affect polyphenol bioactivity, highlighting gaps in knowledge. The implications of extending the use of polyphenols to treat specific pathogenic infections and other illnesses is explored. Full article
(This article belongs to the Special Issue Modulation of Gut Microbiota & Microbiome in Pigs)
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