Topical Collection "Feature Papers in Gut Microbiota"

A topical collection in Microorganisms (ISSN 2076-2607). This collection belongs to the section "Gut Microbiota".

Editor

Prof. Dr. Martin Von Bergen
E-Mail Website
Collection Editor
Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
Interests: microbial ecology; biodegradation of pollutants; metaproteomics; microbial physiology
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

As follows from the title, this Topical Collection “Feature Papers in Gut Microbiota” aims to collect high quality research articles, short communications, and review articles in all the fields of Gut Microbiota.

For the selected works of this section on Gut Microbiota, we will focus on research questions that address the microbial ecology in the community, the functionalities of members of the microbiota, the metabolic and immunological interaction with the host and the role of the microbiota in human diseases.

Topics include, but are not limited to:

  • Structure and function of the microbiota
  • Microbial community genetics, transcriptomics, proteomics and metabolomics
  • Interaction within the microbiota
  • Metabolic interaction with the host
  • Inflammatory diseases
  • Interaction with the immune system
  • Microbial biodegradation of nutrients and xenobiotics
  • Microbial ecology
  • Microbial functions in the different habitats within the gut
  • Metabolic flux analysis
  • Analysis of functionalities by stable isotope probing (DNA, RNA and protein)
  • Model systems for studying microbiome biology
  • Novel technologies for the analysis of structure and function of the microbiota

Prof. Dr. Martin von Bergen
Collection 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 papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection 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. Microorganisms 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 2000 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.

Published Papers (11 papers)

2021

Jump to: 2020, 2019

Article
Alteration of the Immune Response and the Microbiota of the Skin during a Natural Infection by Vibrio harveyi in European Seabass (Dicentrarchus labrax)
Microorganisms 2021, 9(5), 964; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050964 - 29 Apr 2021
Viewed by 672
Abstract
Disease outbreaks continue to represent one of the main bottlenecks for the sustainable development of the aquaculture industry. In marine aquaculture, many species from the Vibrio genus are serious opportunistic pathogens responsible for significant losses to producers. In this study, the effects on [...] Read more.
Disease outbreaks continue to represent one of the main bottlenecks for the sustainable development of the aquaculture industry. In marine aquaculture, many species from the Vibrio genus are serious opportunistic pathogens responsible for significant losses to producers. In this study, the effects on the immune response and the skin microbiota of European sea bass (Dicentrarchus labrax) were studied after a natural disease outbreak caused by V. harveyi. Data obtained from infected and non-infected fish were studied and compared. Regarding the local immune response (skin mucus) a decrease in the protease activity was observed in infected fish. Meanwhile, at a systemic level, a decrease in protease and lysozyme activity was reported while peroxidase activity showed a significant increase in serum from infected fish. A clear dysbiosis was observed in the skin mucus microbiota of infected fish in comparison with non-infected fish. Moreover, V. harveyi, was identified as a biomarker for the infected group and Rubritalea for healthy fish. This study highlights the importance of characterizing the mucosal surfaces and microbial composition of the skin mucus (as a non-invasive technique) to detect potential disease outbreaks in fish farms. Full article
Show Figures

Figure 1

2020

Jump to: 2021, 2019

Article
The Dysbiosis of Gut Microbiota Caused by Low-Dose Cadmium Aggravate the Injury of Mice Liver through Increasing Intestinal Permeability
Microorganisms 2020, 8(2), 211; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020211 - 05 Feb 2020
Cited by 12 | Viewed by 1308
Abstract
Cadmium (Cd), widely present in food and drinking water at low doses, can cause health risks. However, the mechanistic effects of long-term Cd exposure at low dose through dietary intake is poorly studied. The aim of this study is to elucidate whether the [...] Read more.
Cadmium (Cd), widely present in food and drinking water at low doses, can cause health risks. However, the mechanistic effects of long-term Cd exposure at low dose through dietary intake is poorly studied. The aim of this study is to elucidate whether the dysbiosis of gut microbiota caused by Cd at an environmental low dose can aggravate the injury of mice liver, and the possible mechanism is investigated. In order to explore the potential underlying mechanism, the analyses of the variation of gut microbiota composition, intestinal permeability, and hepatic transcriptome were conducted. Our results showed that gut microbiota was disturbed. The rise of intestinal permeability induced by the dysbiosis of gut microbiota resulted in more Cd ions accumulating in mice liver, but it could be restored partly through depleting gut microbiota by antibiotics cocktail. Transcriptomic analyses indicated that 162 genes were significantly differentially expressed including 59 up-regulated and 103 down-regulated in Cd treatment. These genes were involved in several important pathways. Our findings provide a better understanding about the health risks of cadmium in the environment. Full article
Show Figures

Figure 1

2019

Jump to: 2021, 2020

Article
Dietary Saccharomyces cerevisiae boulardii CNCM I-1079 Positively Affects Performance and Intestinal Ecosystem in Broilers during a Campylobacter jejuni Infection
Microorganisms 2019, 7(12), 596; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7120596 - 21 Nov 2019
Cited by 8 | Viewed by 1688
Abstract
In poultry production, probiotics have shown promise to limit campylobacteriosis at the farm level, the most commonly reported zoonosis in Europe. The aim of this trial was to evaluate the effects of Saccharomyces supplementation in Campylobacter jejuni challenged chickens on performance and intestinal [...] Read more.
In poultry production, probiotics have shown promise to limit campylobacteriosis at the farm level, the most commonly reported zoonosis in Europe. The aim of this trial was to evaluate the effects of Saccharomyces supplementation in Campylobacter jejuni challenged chickens on performance and intestinal ecosystem. A total of 156 day old male Ross 308 chicks were assigned to a basal control diet (C) or to a Saccharomyces cerevisiae boulardii CNCM I-1079 supplemented diet (S). All the birds were orally challenged with C. jejuni on day (d) 21. Live weight and growth performance were evaluated on days 1, 21, 28 and 40. The histology of intestinal mucosa was analyzed and the gut microbiota composition was assessed by 16S rRNA. Performance throughout the trial as well as villi length and crypt depth were positively influenced by yeast supplementation. A higher abundance of operational taxonomic units (OTUs) annotated as Lactobacillus reuteri and Faecalibacterium prausnitzii and a lower abundance of Campylobacter in fecal samples from S compared to the C group were reported. Supplementation with Saccharomyces cerevisiae boulardii can effectively modulate the intestinal ecosystem, leading to a higher abundance of beneficial microorganisms and modifying the intestinal mucosa architecture, with a subsequent improvement of the broilers’ growth performance. Full article
Show Figures

Figure 1

Article
The Effect of Maternal Postpartum Practices on Infant Gut Microbiota: A Chinese Cohort Study
Microorganisms 2019, 7(11), 511; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110511 - 30 Oct 2019
Cited by 6 | Viewed by 1438
Abstract
(1) Background: The human gut microbiota at early life is shaped by numerous factors, especially factors from mothers, which have huge influence on infants’ gut microbiotas. The aim of this study was to investigate the effect of maternal adherence to Chinese traditional postpartum [...] Read more.
(1) Background: The human gut microbiota at early life is shaped by numerous factors, especially factors from mothers, which have huge influence on infants’ gut microbiotas. The aim of this study was to investigate the effect of maternal adherence to Chinese traditional postpartum practices of “doing the month” on the development of infant gut microbiota at 6-month postpartum. (2) Methods: A cohort of 62 Chinese women at late pregnancy was recruited from a tertiary general hospital in a central region of China. The participants and their babies were followed up to 6 months postpartum. Finally, 50 mother-infant dyads were enrolled in the study. Women’s adherence to the traditional postpartum practices was measured by adherence to doing the month practices (ADP). Infant fecal samples were collected at six months of age and were analyzed using 16S rRNA V3 and V4 gene region sequences. (3) Results: Ruminococcus gnavus was significantly less abundant in infants whose mothers had a better adherence to the traditional postpartum practices of “doing the month.” Infants receiving Clostridium-butyricum during the first month after delivery had a significant dominance of Escherichia/Shigella. (4) Conclusions: Adherence to the traditional postpartum practices of “doing the month” can impact an infant’s gut microbiota at 6 months of age. Infants receiving probiotics during the first month after delivery had a significant dominance of opportunistic pathogens. Full article
Show Figures

Figure 1

Article
The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?
Microorganisms 2019, 7(10), 393; https://doi.org/10.3390/microorganisms7100393 - 26 Sep 2019
Cited by 8 | Viewed by 1751
Abstract
Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, [...] Read more.
Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile. Although most pipelines reported the same trends in this case-control study, we demonstrated how the use of different pipelines affects the biological conclusions that can be drawn. Targeted metagenomics must therefore rather be considered as a profiling tool to obtain a broad sense of the variations of the microbiota, rather than an accurate identification tool. Full article
Show Figures

Figure 1

Article
Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets
Microorganisms 2019, 7(9), 343; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7090343 - 12 Sep 2019
Cited by 23 | Viewed by 1959
Abstract
Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning [...] Read more.
Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the present study was to bring additional information about the piglet bacterial and archaeal microbiota throughout the entire digestive tract, both at the structural level by using quantitative PCR and high-throughput sequencing, and on functionality by measurement of short-chain fatty acids and predictions using Tax4Fun tool. Our results highlighted strong structural and functional differences between microbial communities inhabiting the fore and the lower gut as well as a quantitatively important archaeal community in the hindgut. The presence of opportunistic pathogens was also noticed throughout the entire digestive tract and could trigger infection emergence. Understanding the role of the intestinal piglet microbiota at weaning could provide further information about the etiology of post-weaning infections and lead to the development of effective preventive solutions. Full article
Show Figures

Graphical abstract

Review
The Role of Gut Microbiota in Intestinal Inflammation with Respect to Diet and Extrinsic Stressors
Microorganisms 2019, 7(8), 271; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080271 - 19 Aug 2019
Cited by 56 | Viewed by 4205
Abstract
The gut microbiota maintains a symbiotic relationship with the host and regulates several important functions including host metabolism, immunity, and intestinal barrier function. Intestinal inflammation and inflammatory bowel disease (IBD) are commonly associated with dysbiosis of the gut microbiota. Alterations in the gut [...] Read more.
The gut microbiota maintains a symbiotic relationship with the host and regulates several important functions including host metabolism, immunity, and intestinal barrier function. Intestinal inflammation and inflammatory bowel disease (IBD) are commonly associated with dysbiosis of the gut microbiota. Alterations in the gut microbiota and associated changes in metabolites as well as disruptions in the intestinal barrier are evidence of the relationship between the gut microbiota and intestinal inflammation. Recent studies have found that many factors may alter the gut microbiota, with the effects of diet being commonly-studied. Extrinsic stressors, including environmental stressors, antibiotic exposure, sleep disturbance, physical activity, and psychological stress, may also play important roles in altering the composition of the gut microbiota. Herein, we discuss the roles of the gut microbiota in intestinal inflammation in relation to diet and other extrinsic stressors. Full article
Show Figures

Figure 1

Article
Dietary Non-Drug Feed Additive as an Alternative for Antibiotic Growth Promoters for Broilers During a Necrotic Enteritis Challenge
Microorganisms 2019, 7(8), 257; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080257 - 13 Aug 2019
Cited by 12 | Viewed by 1576
Abstract
Necrotic enteritis, caused by Clostridium perfringens, is an enteric disease that leads to poor performance and increased mortality, resulting in significant economic losses in poultry production. This study evaluated the effects of a proprietary prebiotic, probiotic, and plant extract blend on performance of [...] Read more.
Necrotic enteritis, caused by Clostridium perfringens, is an enteric disease that leads to poor performance and increased mortality, resulting in significant economic losses in poultry production. This study evaluated the effects of a proprietary prebiotic, probiotic, and plant extract blend on performance of broilers during coccidiosis challenge leading to necrotic enteritis (NE). In total, 744 Cobb500 male broilers were randomly allocated to 3 treatments (8 replicates, 31 birds/pen) including, the negative control (NC) fed a basal diet; the positive control (PC) fed a basal diet with Virginiamycin; and the additive group fed basal diet with a blend of prebiotic, probiotic, and plant extract (BSN). A unique, naturally occurring NE model developed to mimic field conditions was implemented to challenge the birds. This model consists of spraying a concentrated commercial coccidiosis vaccine on litter and feed upon bird placement, which, in conjunction with the presence of C. perfringens spores in the environment, leads to the development of a NE outbreak one week post vaccine application. At the onset of NE on d7, three birds/pen were selected for scoring NE lesions. Body weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) were recorded on days 7, 14, 28, and 42. Carcass composition was assessed by dual energy X-ray absorptiometry (DXA) analysis on day 42. Dietary supplementation of BSN significantly (p < 0.05) improved FCR during starter and grower periods. Dietary treatments had no effect on NE lesions in the small intestine. DXA analysis revealed slightly higher lean content in BSN birds compared to NC. These results showed that dietary supplementation of the BSN blend significantly improved broilers performance during the early NE challenge phase, as well as in the grower period. Full article
Show Figures

Figure 1

Article
Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects
Microorganisms 2019, 7(8), 251; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080251 - 10 Aug 2019
Cited by 18 | Viewed by 2253
Abstract
Escherichia coli may innocuously colonize the intestine of healthy subjects or may instigate infections in the gut or in other districts. This study investigated intestinal E. coli isolated from 20 healthy adults. Fifty-one strains were genotyped by molecular fingerprinting and analyzed for genetic [...] Read more.
Escherichia coli may innocuously colonize the intestine of healthy subjects or may instigate infections in the gut or in other districts. This study investigated intestinal E. coli isolated from 20 healthy adults. Fifty-one strains were genotyped by molecular fingerprinting and analyzed for genetic and phenotypic traits, encompassing the profile of antibiotic resistance, biofilm production, the presence of surface structures (such as curli and cellulose), and their performance as recipients in conjugation experiments. A phylogroup classification and analysis of 34 virulence determinants, together with genes associated to the pks island (polyketide-peptide genotoxin colibactin) and conjugative elements, was performed. Most of the strains belonged to the phylogroups B1 and B2. The different phylogroups were separated in a principal coordinate space, considering both genetic and functional features, but not considering pulsed-field gel electrophoresis. Within the B2 and F strains, 12 shared the pattern of virulence genes with potential uropathogens. Forty-nine strains were sensitive to all the tested antibiotics. Strains similar to the potential pathogens innocuously inhabited the gut of healthy subjects. However, they may potentially act as etiologic agents of extra-intestinal infections and are susceptible to a wide range of antibiotics. Nevertheless, there is still the possibility to control infections with antibiotic therapy. Full article
Show Figures

Graphical abstract

Review
The Revival of the Battle between David and Goliath in the Enteric Viruses and Microbiota Struggle: Potential Implication for Celiac Disease
Microorganisms 2019, 7(6), 173; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7060173 - 14 Jun 2019
Cited by 9 | Viewed by 1923
Abstract
The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the [...] Read more.
The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. Since the virome can impact microbial genetics and behavior, understanding its biology, composition, cellular cycle, regulation, mode of action and potential beneficial or hostile activities can change the present paradigm of the cross-talks in the luminal gut compartment. Celiac disease is a frequent autoimmune disease in which viruses can play a role in disease development. Based on the current knowledge on the enteric virome, in relation to celiac disease pathophysiological evolvement, the current review summarizes the potential interphases between the two. Exploring and understanding the role of the enteric virome in gluten-dependent enteropathy might bring new therapeutic strategies to change the luminal eco-event for the patient’s benefit. Full article
Show Figures

Figure 1

Review
Probiotics and Prebiotics for the Amelioration of Type 1 Diabetes: Present and Future Perspectives
Microorganisms 2019, 7(3), 67; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7030067 - 02 Mar 2019
Cited by 35 | Viewed by 4726
Abstract
Type 1-diabetes (T1D) is an autoimmune disease characterized by immune-mediated destruction of pancreatic beta (β)-cells. Genetic and environmental interactions play an important role in immune system malfunction by priming an aggressive adaptive immune response against β-cells. The microbes inhabiting the human intestine closely [...] Read more.
Type 1-diabetes (T1D) is an autoimmune disease characterized by immune-mediated destruction of pancreatic beta (β)-cells. Genetic and environmental interactions play an important role in immune system malfunction by priming an aggressive adaptive immune response against β-cells. The microbes inhabiting the human intestine closely interact with the enteric mucosal immune system. Gut microbiota colonization and immune system maturation occur in parallel during early years of life; hence, perturbations in the gut microbiota can impair the functions of immune cells and vice-versa. Abnormal gut microbiota perturbations (dysbiosis) are often detected in T1D subjects, particularly those diagnosed as multiple-autoantibody-positive as a result of an aggressive and adverse immunoresponse. The pathogenesis of T1D involves activation of self-reactive T-cells, resulting in the destruction of β-cells by CD8+ T-lymphocytes. It is also becoming clear that gut microbes interact closely with T-cells. The amelioration of gut dysbiosis using specific probiotics and prebiotics has been found to be associated with decline in the autoimmune response (with diminished inflammation) and gut integrity (through increased expression of tight-junction proteins in the intestinal epithelium). This review discusses the potential interactions between gut microbiota and immune mechanisms that are involved in the progression of T1D and contemplates the potential effects and prospects of gut microbiota modulators, including probiotic and prebiotic interventions, in the amelioration of T1D pathology, in both human and animal models. Full article
Show Figures

Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

The impact of the metagenomic bioinformatics pipeline: does the "microscope" affect the paradigm in metagenomic analyses?

Authors: Magali Chabé, et al.

 

Microbiota composition and functional profiling throughout the gastrointestinal tract of commercial weaning piglets

Authors: Raphaele Gresse, Frédérique Chaucheyras-Durand, et al.

 

Host-microbiota interaction through metabolites and epithelial cells

Authors: Yun Kyung Lee, et al.

 

Dietary natural feed additive as an alternative for antibiotic growth promoters in broilers during a necrotic enteritis challenge

Authors: Rami A. Dalloul, et al.
Back to TopTop