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Special Issue "Gut Microbiota and the Impact on Animal Models of Disease"

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 13349

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Dr. James Amos-Landgraf

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Guest Editor

Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201, USA
Interests: gut microbiota; colon cancer; animal model; genetics; epigenetics; metagenomics

Special Issue Information

Dear Colleagues,

During the past decade, it has become increasing clear that the commensal gut microbiota performs a delicate balancing act with its host, playing a nearly indispensable role in nutritional metabolism on the one hand, and creating a community that increases one’s risk to developing disease. While many pathogenic bacteria with clear toxic pathways have been identified, the role of commensal microbes in disease susceptibility is not understood as well. Recent studies in animal models of intestinal cancer in an otherwise specific pathogen-free environment have shown differential susceptibility to disease associated with different complex gut microbiota. There are many putative genera that associate with either increased or decreased risk. It is becoming clearer that single microbes may not be a specific cause, but rather complex combinations and interactions altering the metabolic profile are likely driving this susceptibility.

The aim of this Special Issue is to begin to resolve the role of microbes in disease development, especially in animal models of disease, and relating that to the larger translational implication to human disease. This can involve many biological systems, including infection and immunity, metabolism, genetic, and epigenetic influences.

We are pleased and excited to invite you to submit to this Special Issue that will address our current understanding of the gut microbiota effects on animal models of disease, with an emphasis on intestinal cancer and metabolic disease models, and strategies to resolve the multiple roles of the animal-associated microbiota.

In this Special Issue, we are welcoming original research articles and reviews. Research areas may include (but are not limited to) the following: gut, skin, vaginal, or other specific microbiota and the biological role in animal models. While the focus will be vertebrate mammals, other species including zebrafish and invertebrate model systems are welcome.

I look forward to receiving your contributions.

Dr. James Amos-Landgraf
Guest Editor

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Open AccessArticle

Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle

Venkata Vinay Kumar Bandarupalli

and

Benoit St-Pierre

Microorganisms 2023, 11(3), 658; https://doi.org/10.3390/microorganisms11030658 - 04 Mar 2023

Viewed by 633

Abstract

In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessArticle

An Archetypical Model for Engrafting Bacteroides fragilis into Conventional Mice Following Reproducible Antibiotic Conditioning of the Gut Microbiota

and

Microorganisms 2023, 11(2), 451; https://doi.org/10.3390/microorganisms11020451 - 10 Feb 2023

Viewed by 761

Abstract

Bacteroides fragilis is a commonly investigated commensal bacterium for its protective role in host diseases. Here, we aimed to develop a reproducible antibiotic-based model for conditioning the gut microbiota and engrafting B. fragilis into a conventional murine host. Initially, we selected different combinations of antibiotics, including metronidazole, imipenem, and clindamycin, and investigated their efficacy in depleting the mouse Bacteroides population. We performed 16S rRNA sequencing of DNA isolated from fecal samples at different time points. The α-diversity was similar in mice treated with metronidazole (MET) and differed only at weeks 1 (p = 0.001) and 3 (p = 0.009) during metronidazole/imipenem (MI) treatment. Bacteroides compositions, during the MET and MI exposures, were similar to the pre-antibiotic exposure states. Clindamycin supplementation added to MET or MI regimens eliminated the Bacteroides population. We next repeated metronidazole/clindamycin (MC) treatment in two additional independent experiments, followed by a B. fragilis transplant. MC consistently and reproducibly eliminated the Bacteroides population. The depleted Bacteroides did not recover in a convalescence period of six weeks post-MC treatment. Finally, B. fragilis was enriched for ten days following engraftment into Bacteroides-depleted mice. Our model has potential use in gut microbiota studies that selectively investigate Bacteroides’ role in diseases of interest. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessArticle

Global Genomic Epidemiology of Escherichia coli (ExPEC) ST38 Lineage Revealed a Virulome Associated with Human Infections

and

Microorganisms 2022, 10(12), 2482; https://doi.org/10.3390/microorganisms10122482 - 15 Dec 2022

Viewed by 725

Abstract

Background: Most of the extraintestinal human infections worldwide are caused by specific extraintestinal pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, a high-risk globally disseminated ExPEC. To get insights on the aspects of the global ST38 epidemiology and evolution as a multidrug-resistant and pathogenic lineage concerning the three axes of the One Health concept (humans, animals, and natural environments), this study performed a global phylogenomic analysis on ST38 genomes. Methods: A phylogenetic reconstruction based on 376 ST38 genomes recovered from environments, humans, livestock, and wild and domestic animals in all continents throughout three decades was performed. The global information concerning the ST38 resistome and virulome was also approached by in silico analyses. Results: In general, the phylogenomic analyses corroborated the zoonotic character of the ExPEC ST38, since clonal strains were recovered from both animal and human sources distributed worldwide. Moreover, our findings revealed that, independent of host sources and geographic origin, the genomes were distributed in two major clades (Clades 1 and 2). However, the ST38 accessory genome was not strictly associated with clades and sub-clades, as found for the type 2 T3SS ETT2 that was evenly distributed throughout Clades 1 and 2. Of note was the presence of the Yersinia pestis-like high-pathogenicity island (HPI) exclusively in the major Clade 2, in which prevails most of the genomes from human origin recovered worldwide (2000 to 2020). Conclusions: This evidence corroborates the HPI association with successful E. coli ST38 establishment in human infections. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessArticle

Hymenolepis diminuta Reduce Lactic Acid Bacterial Load and Induce Dysbiosis in the Early Infection of the Probiotic Colonization of Swiss Albino Rat

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Microorganisms 2022, 10(12), 2328; https://doi.org/10.3390/microorganisms10122328 - 24 Nov 2022

Viewed by 1137

Abstract

Tapeworm infection continues to be an important cause of morbidity worldwide. Recent metagenomics studies have established a link between gut microbiota and parasite infection. The identification of gut probiotics is of foremost importance to explore its relationship and function with the parasite in the host. In this study, the gut content of hosts infected with tapeworm Hymenolepis diminuta and non-infected host gut were disected out to determine their Lactic acid bacterial (LAB) population in MRS agar and microbial community was analysed by metagenomics. The bacterial count was calculated on a bacterial counting chamber and their morphology was determined microscopically and biochemically. Further, to determine the safety profile antibiotic resistance test, antimicrobial, hemolytic activity, and adhesion capability were calculated. We found six dominant probiotic strains and a decrease in LAB load from 1.7–2.3 × 10⁷ CFU/mL in the uninfected group to a range of 8.4 × 10⁵ CFU/mL to 3.2 × 10⁵ CFU/mL in the infected groups with respect to an increase in the parasite number from 10–18. In addition, we found a depletion in the probiotic relative abundance of Lactobacillus and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria, and Streptococcus. Phylogenetic analysis of the six probiotics revealed a close similarity with different strains of L. brevis, L. johnsonii, L. taiwansis, L. reuteri, L. plantarum, and L. pentosus. Thus, this study suggests that the parasite inhibits probiotic colonization in the gut during its early establishment of infection inside the host. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessArticle

Gut Microbiome Alteration after Reboxetine Administration in Type-1 Diabetic Rats

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Microorganisms 2021, 9(9), 1948; https://doi.org/10.3390/microorganisms9091948 - 14 Sep 2021

Cited by 2 | Viewed by 2066

Abstract

Antidepressants are drugs commonly used in clinical settings. However, there are very limited studies on the effects of these drugs on the gut microbiota. Herein, we evaluated the effect of reboxetine (RBX), a selective norepinephrine (noradrenaline) reuptake inhibitor (NRI), on gut microbiota in both diabetic and non-diabetic rats. This is the first report of relation between reboxetine use and the gut microbiota to our knowledge. In this study, type-1 diabetes induced by using streptozotocin (STZ) and RBX was administered to diabetic rats and healthy controls for 14 days. At the end of the treatment, stool samples were collected. Following DNA extraction, amplicon libraries for the V3-V4 region were prepared and sequenced with the Illumina Miseq platform. QIIME was used for preprocessing and analysis of the data. As a result, RBX had a significant effect on gut microbiota structure and composition in diabetic and healthy rats. For example, RBX exposure had a pronounced microbial signature in both groups, with a low Firmicutes/Bacteroidetes ratio and low Lactobacillus levels. While another abundance phylum after exposure to RBX was Proteabacteria, other notable taxa in the diabetic group included Flavobacterium, Desulfovibrionaceae, Helicobacteriaceae, Campylobacterales, and Pasteurellacae when compared to the untreated group. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessArticle

Age and Giardia intestinalis Infection Impact Canine Gut Microbiota

and

Luis G. Bermúdez-Humarán

Microorganisms 2021, 9(9), 1862; https://doi.org/10.3390/microorganisms9091862 - 02 Sep 2021

Cited by 3 | Viewed by 2381

Abstract

Giardia intestinalis is a flagellated protozoan responsible for giardiosis (also called giardiasis in humans), the most prevalent and widespread parasitic infection in humans and mammals worldwide. The intestinal microbiota is highly diverse and any alteration in its composition may impact on the health of the host. While studies on the mouse model of giardiosis described the role of the gut microbiota in host susceptibility to infection by the parasite, little is known about the gut microbiota during natural infections in dogs and particularly in puppies. In this study, we monitored naturally G. intestinalis-infected puppies for 3 months and quantified cyst excretion every 2 weeks. All puppies remained subclinically infected during the sampling period as confirmed by fecal examination. In parallel, we performed 16S Illumina sequencing of fecal samples from the different time points to assess the impact of G. intestinalis infection on gut microbiota development of the puppies, as well as gut health markers of immunity such as fecal IgA and calprotectin. Sequencing results revealed that the canine fecal microbiota of Giardia-infected puppies becomes more complex and less diverse with increasing age. In addition, significant differences in the structure of the microbiota were observed between puppies with high and low Giardia cyst excretion. Chronic subclinical G. intestinalis infection appears to be associated with some detrimental structural changes in the gut microbiota. G. intestinalis-associated dysbiosis is characterized by an enrichment of facultative anaerobic, mucus-degrading, pro-inflammatory species and opportunistic pathogens, as well as a reduction of Lactobacillus johnsonii at specific time points. Calprotectin levels increased with age, suggesting the establishment of chronic low-grade inflammation in puppies. Further work is needed to demonstrate whether these alterations in the canine gut microbiota could lead to a dysbiosis-related disease, such as irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD). Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessArticle

Adherent-Invasive and Non-Invasive Escherichia coli Isolates Differ in Their Effects on Caenorhabditis elegans’ Lifespan

Maria Beatriz de Sousa Figueiredo

and

Microorganisms 2021, 9(9), 1823; https://doi.org/10.3390/microorganisms9091823 - 27 Aug 2021

Cited by 4 | Viewed by 1593

Abstract

The adherent-invasive Escherichia coli (AIEC) pathotype has been implicated in the pathogenesis of inflammatory bowel diseases in general and in Crohn’s disease (CD) in particular. AIEC strains are primarily characterized by their ability to adhere to and invade intestinal epithelial cells. However, the genetic and phenotypic features of AIEC isolates vary greatly as a function of the strain’s clonality, host factors, and the gut microenvironment. It is thus essential to identify the determinants of AIEC pathogenicity and understand their role in intestinal epithelial barrier dysfunction and inflammation. We reasoned that soil nematode Caenorhabditis elegans (a simple but powerful model of host-bacterium interactions) could be used to study the virulence of AIEC vs. non- AIEC E. coli strains. Indeed, we found that the colonization of C. elegans (strain N2) by E. coli impacted survival in a strain-specific manner. Moreover, the AIEC strains’ ability to invade cells in vitro was linked to the median lifespan in C. elegans (strain PX627). However, neither the E. coli intrinsic invasiveness (i.e., the fact for an individual strain to be characterized as invasive or not) nor AIEC’s virulence levels (i.e., the intensity of invasion, established in % from the infectious inoculum) in intestinal epithelial cells was correlated with C. elegans’ lifespan in the killing assay. Nevertheless, AIEC longevity of C. elegans might be a relevant model for screening anti-adhesion drugs and anti-invasive probiotics. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessReview

Rumen Biogeographical Regions and Microbiome Variation

Macey P. Soltis

Sarah E. Moorey

Amanda M. Egert-McLean

Brynn H. Voy

Elizabeth A. Shepherd

and

Phillip R. Myer

Microorganisms 2023, 11(3), 747; https://doi.org/10.3390/microorganisms11030747 - 14 Mar 2023

Viewed by 1270

Abstract

The rumen is a complex organ that is critical for its host to convert low-quality feedstuffs into energy. The conversion of lignocellulosic biomass to volatile fatty acids and other end products is primarily driven by the rumen microbiome and its interaction with the host. Importantly, the rumen is demarcated into five distinct rumen sacs as a result of anatomical structure, resulting in variable physiology among the sacs. However, rumen nutritional and microbiome studies have historically focused on the bulk content or fluids sampled from single regions within the rumen. Examining the rumen microbiome from only one or two biogeographical regions is likely not sufficient to provide a comprehensive analysis of the rumen microbiome and its fermentative capacity. Rumen biogeography, digesta fraction, and microbial rumen–tissue association all impact the diversity and function of the entirety of the rumen microbiome. Therefore, this review discusses the importance of the rumen biographical regions and their contribution to microbiome variation. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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Open AccessReview

Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens

Frédérique Chaucheyras-Durand

Audrey Sacy

Kip Karges

and

Emmanuelle Apper

Microorganisms 2022, 10(12), 2517; https://doi.org/10.3390/microorganisms10122517 - 19 Dec 2022

Cited by 1 | Viewed by 1690

Abstract

Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a broad range of various microorganisms, differing in each GIT segment, which are essential for efficient utilization of feed, especially to use nutrients that are not or little degraded by endogenous enzymes. In addition, like in other animal species, the GIT microbiota is in permanent interplay with the host’s cells and is involved in a lot of functions among which inflammation, immune homeostasis, and energy metabolism. As for other animals and humans, the horse gut microbiome is sensitive to diet, especially consumption of starch, fiber, and fat. Age, breeds, stress during competitions, transportation, and exercise may also impact the microbiome. Because of its size and its complexity, the equine GIT microbiota is prone to perturbations caused by external or internal stressors that may result in digestive diseases like gastric ulcer, diarrhea, colic, or colitis, and that are thought to be linked with systemic diseases like laminitis, equine metabolic syndrome or obesity. Thus, in this review we aim at understanding the common core microbiome -in terms of structure and function- in each segment of the GIT, as well as identifying potential microbial biomarkers of health or disease which are crucial to anticipate putative perturbations, optimize global practices and develop adapted nutritional strategies and personalized nutrition. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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