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Microorganisms
Special Issues
Regulation and Workings of the Gastrointestinal Microbiota
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Regulation and Workings of the Gastrointestinal Microbiota

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

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 9947

Special Issue Editor

Dr. Gilles R. G. Monif

E-Mail Website
Guest Editor
Infectious Diseases Incorporated, Bellevue, NE 68123, USA
Interests: gastrointestinal microbiota; crohn's disease; bacterial regulation

Special Issue Information

Dear Colleagues,

The human gastrointestinal tract is an evolutionary adaptation of the one-cell amoeba. The amoeba’s outer cell wall affords it protection from hostile environment elements, yet it still allows the ingress of needed nutrients and egress of their counterproductive metabolites. Accommodation of ingress and egress introduced a layer of vulnerability that required the development of a compensatory defense mechanism in the form of local and systemic immune system governance.

By design, the initial human bacterial flora is acquired during birthing from the bacterial flora of the female vagina. This inoculum initiates the body’s acquired immunity. The importance of anaerobic lactobacillus being the inoculum controller is inferred by the apparent enhanced immunity of infants delivered vaginally versus those delivered by Cesarean section. The importance of aerobic lactobacilli in governance of the gastrointestinal microbiota is further inferred by the observation that when attempts are made to re-regulate gastrointestinal dysbiosis by using probiotics, only probiotics composed aerobic lactobacillus have had demonstrated clinical efficacy.

To understand bacterial governance of the gastrointestinal microbiota, one must comprehend those that function to regulate the bacterial constituency of the female genital tract. The basic stability of its oxidation/reduction potential and the paucity of exogenous bacterial challenges facilitate the identification of underlying mechanisms of bacterial governance.

Why has the gastrointestinal microbiota been such an enigma to understand is the inability to control variables that influence the oxidation/reduction potential of the microbiological environment. The gastrointestinal mucosa and intraluminal bacterial microbiota interface can be viewed as two separate nations whose apposition is the product of evolution that put a biased priority on the stability of the resultant commensal/symbiotic relationship. Bacterial pathogenicity constitutes a de-stabilization force and, as such, is counter-productive to the overall schema. Both entities have developed well-defined mechanisms to address microbial pathogenicity. Current research needs to focus on improving the understanding of these mechanisms.

In this Special Issue, research areas may include (but are not limited to) the following:

  • Composition of the Gastrointestinal Microbiota;
  • Immunology of the Gastrointestinal Tract/Immunological Regulation of the Gastrointestinal Microbiota;
  • Mechanisms of Bacterial Interference;
  • Crohn’s Disease;
  • Clostridium difficile in Health and Disease;
  • Fecal Therapy;
  • Probiotics.

Dr. Gilles R. G. Monif
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. 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 2700 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

  • gastrointestinal microbiota
  • bacterial interference
  • bacterial regulation
  • lactobacilli

Published Papers (4 papers)

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Research

26 pages, 3341 KiB  
Article
Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183
by Abhishek Bhattacharya, Lovisa Majtorp, Simon Birgersson, Mathias Wiemann, Krishnan Sreenivas, Phebe Verbrugghe, Olivier Van Aken, Ed W. J. Van Niel and Henrik Stålbrand
Microorganisms 2022, 10(12), 2496; https://doi.org/10.3390/microorganisms10122496 - 16 Dec 2022
Cited by 2 | Viewed by 2017
Abstract
β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated [...] Read more.
β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated the cross-feeding and metabolic interactions between Bifidobacterium adolescentis ATCC 15703, an acetate producer, and Roseburia hominis A2-183 DSMZ 16839, a butyrate producer, during utilization of MOS/GMOSs. Cocultivation studies suggest that both strains coexist due to differential MOS/GMOS utilization, along with the cross-feeding of acetate from B. adolescentis E194a to R. hominis A2-183. The data suggest that R. hominis A2-183 efficiently utilizes MOS/GMOS in mono- and cocultivation. Notably, we observed the transcriptional upregulation of certain genes within a dedicated MOS/GMOS utilization locus (RhMosUL), and an exo-oligomannosidase (RhMan113A) gene located distally in the R. hominis A2-183 genome. Significantly, biochemical analysis of β-1,4 mannan-oligosaccharide phosphorylase (RhMOP130A), α-galactosidase (RhGal36A), and exo-oligomannosidase (RhMan113A) suggested their potential synergistic role in the initial utilization of MOS/GMOSs. Thus, our results enhance the understanding of MOS/GMOS utilization by potential health-promoting human gut microbiota and highlight the role of cross-feeding and metabolic interactions between two secondary mannan degraders inhabiting the same ecological niche in the gut. Full article
(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)
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15 pages, 3294 KiB  
Article
Promotion of Deoxycholic Acid Effect on Colonic Cancer Cell Lines In Vitro by Altering the Mucosal Microbiota
by Yanpeng Ma, Yi Zhang, Ruize Qu, Xin Zhou, Lulu Sun, Kai Wang, Changtao Jiang, Zhipeng Zhang and Wei Fu
Microorganisms 2022, 10(12), 2486; https://doi.org/10.3390/microorganisms10122486 - 15 Dec 2022
Cited by 3 | Viewed by 1732
Abstract
Colorectal cancer (CRC) is the third most prevalent neoplasm and the second leading cause of cancer death worldwide. Microbiota and their products, such as bile acids (BAs), are important causal factors for the occurrence and development of CRC. Therefore, we performed 16S ribosomal [...] Read more.
Colorectal cancer (CRC) is the third most prevalent neoplasm and the second leading cause of cancer death worldwide. Microbiota and their products, such as bile acids (BAs), are important causal factors for the occurrence and development of CRC. Therefore, we performed 16S ribosomal RNA (16S rRNA) and liquid chromatography/mass spectrometry (LC–MS) to measure mucosal microbiota and BA composition in paired cancerous and noncancerous gut tissue samples from 33 patients with CRC at a hospital in Beijing. In cancerous tissues, we detected altered mucosal microbiota with increased levels of the genera Bacteroides, Curtobacterium, and Campylobacter and an increase in deoxycholic acid (DCA), which was the only BA elevated in cancerous tissues. Ex vivo coculture showed that the mucosal microbiota in cancerous tissues indeed had a stronger DCA production ability, indicating that DCA-producing bacteria are enriched in tumors. Results from the CCK8 and Transwell assays indicated that DCA enhances the overgrowth, migration, and invasion of CRC cell lines, and, through qPCR and Western blot analyses, downregulation of FXR was observed in CRC cell lines after DCA culture. We then verified the downregulation of FXR expression in cancerous tissues using our data and the TCGA database, and we found that FXR downregulation plays an important role in the development of CRC. In conclusion, differing mucosal microbiota, increased amounts of mucosal DCA, and lower FXR expression were demonstrated in cancerous tissues compared to normal tissue samples. The results of this study can be applied to the development of potential therapeutic targets for CRC prevention, such as altering mucosal microbiota, DCA, or FXR. Full article
(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)
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13 pages, 2383 KiB  
Article
Bile Acids: Major Regulator of the Gut Microbiome
by Chihyeok An, Hyeyeon Chon, Wanrim Ku, Sunho Eom, Mingyu Seok, Sangha Kim, Jaesun Lee, Daesung Kim, Sanghyuk Lee, Hoonsup Koo, Hyunjung Cho, Seungyun Han, Juik Moon, Miil Kang and Kihyun Ryu
Microorganisms 2022, 10(9), 1792; https://doi.org/10.3390/microorganisms10091792 - 06 Sep 2022
Cited by 9 | Viewed by 3754
Abstract
Bile acids are synthesized from cholesterol and play an important role in regulating intestinal microflora. The different degrees of hydrophobicity and acidity of individual bile acids may affect their antimicrobial properties. We examined the antimicrobial effects of different bile acids on various microorganisms [...] Read more.
Bile acids are synthesized from cholesterol and play an important role in regulating intestinal microflora. The different degrees of hydrophobicity and acidity of individual bile acids may affect their antimicrobial properties. We examined the antimicrobial effects of different bile acids on various microorganisms in vitro and confirmed whether these remain consistent in vivo. Using human bile acids, including ursodeoxycholic acid, cholic acid, chenodeoxycholic acid, deoxycholic acid, and lithocholic acid, a disc diffusion test was performed, and a rodent model was created to determine the antimicrobial effects of each bile acid. The fecal bacterial population was analyzed using a real-time polymerase chain reaction. Each bile acid showed different microbial inhibitory properties. The inhibitory activity of bile acids against microbiota which normally resides in the gastrointestinal tract and biliary system, was low; however, normal flora of other organs was significantly inhibited. Changes in microbial counts after bile acid administration in a rodent model differed in the colon and cecum. The in vivo and in vitro results show that the antimicrobial effects of bile acids against intestinal microbiota were similar. In conclusion, bile acids could be a novel treatment strategy to regulate gut microbiota. Full article
(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)
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12 pages, 1755 KiB  
Article
The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture
by Vladimir A. Veselovsky, Marina S. Dyachkova, Dmitry A. Bespiatykh, Roman A. Yunes, Egor A. Shitikov, Polina S. Polyaeva, Valeriy N. Danilenko, Evgenii I. Olekhnovich and Ksenia M. Klimina
Microorganisms 2022, 10(8), 1683; https://doi.org/10.3390/microorganisms10081683 - 21 Aug 2022
Cited by 8 | Viewed by 1963
Abstract
To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the [...] Read more.
To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the host, it is important to study them using transcriptomics. In this study, we applied the RNA-Seq technique to study global gene expression of B. longum at different growth phases in order to better understand the response of bifidobacterial cells to the specific conditions of the human gut. We have shown that in the lag phase, ABC transporters, whose function may be linked to active substrate utilization, are increasingly expressed due to preparation for cell division. In the exponential phase, the functions of activated genes include synthesis of amino acids (alanine and arginine), energy metabolism (glycolysis/gluconeogenesis and nitrogen metabolism), and translation, all of which promote active cell division, leading to exponential growth of the culture. In the stationary phase, we observed a decrease in the expression of genes involved in the control of the rate of cell division and an increase in the expression of genes involved in defense-related metabolic pathways. We surmise that the latter ensures cell survival in the nutrient-deprived conditions of the stationary growth phase. Full article
(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)
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