Beneficial Microbes and Gastrointestinal Microbiota, 2nd Edition

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

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 9985

Special Issue Editor


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Guest Editor
Food Research & Innovation Centre, College of Science, Engineering and Health, RMIT University, Melbourne, Australia
Interests: gut microbiome; probiotics and prebiotics; fermented foods; food safety; metabolomics; intestinal and respiratory infections and antimicrobials
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of the Special Issue “Beneficial Microbes and Gastrointestinal Microbiota”(https://www.mdpi.com/journal/microorganisms/special_issues/beneficial_microbes_gastrointestinal_microbiota).

Human gut epithelial surfaces are colonized and safeguarded by tremendous numbers of microorganisms, known as gastrointestinal microflora, which are crucial for forming and balancing complex microbial ecosystems. These diverse microorganisms, especially beneficial microbes, are essential for the gastrointestinal health and immunity of the hosts. However, factors such as malnutrition, immunodeficiency, and antibiotic therapy can induce dysbiosis of the gut microbial ecosystem, further inducing or leading to the deterioration of intestinal disorders and diseases, such as antibiotic-associated diarrhea, inflammatory bowel disease, ulcerative colitis, and even colorectal cancer. Over the last decade, we have witnessed spectacular research progress in identifying the functional roles of probiotics in human gastrointestinal health and applying probiotics for restoring homeostatic gut microbiota.

This Special Issue entitled “Beneficial Microbes and Gastrointestinal Microbiota” aims to present the most recent and cutting-edge research on all aspects relevant to the connection and interactions between probiotics, the gut microbiome, and intestinal health. We kindly invite the research community to submit original articles that provide novel insights into topics including, but not limited to, the following:

  • Probiotics and postbiotics in modulating the gastrointestinal microbiota and immunity;
  • Establishment and effectiveness of functional foods containing bioactive probiotic strains;
  • Novel efficient pro-commensal strategies to improve gastrointestinal health;
  • Metabolic and biofunctional enhancement of beneficial microbes;
  • Bacterial consortium for restoration of gut intestinal microbiota and treatment of enteric diseases.

Prof. Dr. Harsharn Gill
Guest Editor

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Keywords

  • probiotics
  • gut microbiome
  • gastrointestinal health
  • intestinal dysbiosis
  • enteric diseases
  • pro-commensal strategy
  • bacterial consortium.

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Published Papers (4 papers)

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Research

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21 pages, 4386 KiB  
Article
Analysis of Characteristics of Bovine-Derived Non-Enterotoxigenic Bacteroides fragilis and Validation of Potential Probiotic Effects
by Dong Wang, Long Zhao, Jingyi Lin, Yajing Wang, Haihui Gao, Wenhui Liu, Qirui Li, Liang Zhang, Xiaodong Kang and Kangkang Guo
Microorganisms 2024, 12(11), 2319; https://doi.org/10.3390/microorganisms12112319 - 14 Nov 2024
Viewed by 1044
Abstract
Bacteroides fragilis is a new generation of probiotics, and its probiotic effects on humans and some animals have been verified. However, research on B. fragilis in cattle is still lacking. In this study, 24 stool samples were collected from two large-scale cattle farms [...] Read more.
Bacteroides fragilis is a new generation of probiotics, and its probiotic effects on humans and some animals have been verified. However, research on B. fragilis in cattle is still lacking. In this study, 24 stool samples were collected from two large-scale cattle farms in Wuzhong, Ningxia, including 12 diarrheal and 12 normal stools. A non-toxigenic Bacteroides fragilis (NTBF) was isolated and identified by 16S rRNA high-throughput sequencing and named BF-1153; genome composition and genome functional analyses were carried out to reflect the biological characteristics of the BF-1153 strain. A cluster analysis of BF-1153 was performed using Mega X to explore its genetic relationship. In addition, Cell Counting Kit-8 (CCK8) was used to determine the toxic effects of the strain on human ileocecal colorectal adenocarcinoma cell line cells (HCT-8), Madin-Darby bovine kidney cells (MDBK), and intestinal porcine epithelial cells (IPECs). The results showed that BF-1153 conformed to the biological characteristics of B. fragilis. BF-1153 had no toxic effects on HCT-8, MDBK, and IPEC. Animal experiments have shown that BF-1153 has no toxic effects on healthy SPF Kunming mice. Notably, the supernatant of BF-1153 enhanced cell activity and promoted cell growth in all three cell lines. At the same time, a cluster analysis of the isolated strains showed that the BF-1153 strain belonged to the same branch as the B. fragilis strain 23212, and B. fragilis strain 22998. The results of the animal experiments showed that BF-1153 had a certain preventive effect on diarrhea symptoms in SPF Kunming mice caused by a bovine rotavirus (BRV). In summary, the strain BF-1153 isolated in this experiment is NTBF, which has no toxic effect on MDBK, HCT-8, and IPEC, and has obvious cell growth-promoting effects, especially on MDBK. BF-1153 promotes the growth and development of SPF Kunming mice when compared with the control group. At the same time, BF-1153 alleviated the diarrhea symptoms caused by BRV in SPF Kunming mice. Therefore, BF-1153 has the potential to be a probiotic for cattle. Full article
(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota, 2nd Edition)
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13 pages, 5419 KiB  
Article
Garlic-Induced Enhancement of Bifidobacterium: Enterotype-Specific Modulation of Gut Microbiota and Probiotic Populations
by Jina Ha, Jinwoo Kim, Seongok Kim, Kwang Jun Lee and Hakdong Shin
Microorganisms 2024, 12(10), 1971; https://doi.org/10.3390/microorganisms12101971 - 28 Sep 2024
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Abstract
The gut microbiome is a dynamic ecosystem crucial for maintaining its host’s health by regulating various immune and metabolic functions. Since diet plays a fundamental role in shaping the gut microbiome, understanding the relationship between food consumption and microbiome structure is essential. Although [...] Read more.
The gut microbiome is a dynamic ecosystem crucial for maintaining its host’s health by regulating various immune and metabolic functions. Since diet plays a fundamental role in shaping the gut microbiome, understanding the relationship between food consumption and microbiome structure is essential. Although medicinal plants are widely recognized for their broad health benefits, their specific impact on the gut microbiome remains unclear. In this study, we investigated the effects of garlic (Allium sativum) on the gut microbiome using an in vitro human fecal incubation model. Our findings revealed that the impact of garlic on gut microbial structure varied depending on the dominant gut microbiome components (enterotypes). The Bacteroides-dominant enterotype exhibited significant changes in overall microbial diversity in response to garlic, while the Prevotella-dominant enterotype remained unaffected. Additionally, the garlic treatment led to specific alterations in microbiota composition, such as an increase in beneficial probiotics like Bifidobacterium. We validated garlic’s prebiotic potential by promoting the growth of Bifidobacterium adolescentis under in vitro culture conditions. Our study highlights the importance of understanding enterotype-specific responses to diet and suggests that garlic may serve as a dietary supplement for modulating gut microbiota and promoting the growth of beneficial probiotics. Full article
(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota, 2nd Edition)
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15 pages, 2252 KiB  
Article
Characterization of Probiotic Properties and Whole-Genome Analysis of Lactobacillus johnsonii N5 and N7 Isolated from Swine
by Kun Wang, Yu Wang, Lifang Gu, Jinyan Yu, Qianwen Liu, Ruiqi Zhang, Guixin Liang, Huan Chen, Fang Gu, Haoyu Liu, Xin’an Jiao and Yunzeng Zhang
Microorganisms 2024, 12(4), 672; https://doi.org/10.3390/microorganisms12040672 - 28 Mar 2024
Cited by 5 | Viewed by 2763
Abstract
In our previous microbiome profiling analysis, Lactobacillus (L.) johnsonii was suggested to contribute to resistance against chronic heat stress-induced diarrhea in weaned piglets. Forty-nine L. johnsonii strains were isolated from these heat stress-resistant piglets, and their probiotic properties were assessed. Strains [...] Read more.
In our previous microbiome profiling analysis, Lactobacillus (L.) johnsonii was suggested to contribute to resistance against chronic heat stress-induced diarrhea in weaned piglets. Forty-nine L. johnsonii strains were isolated from these heat stress-resistant piglets, and their probiotic properties were assessed. Strains N5 and N7 exhibited a high survival rate in acidic and bile environments, along with an antagonistic effect against Salmonella. To identify genes potentially involved in these observed probiotic properties, the complete genome sequences of N5 and N7 were determined using a combination of Illumina and nanopore sequencing. The genomes of strains N5 and N7 were found to be highly conserved, with two N5-specific and four N7-specific genes identified. Multiple genes involved in gastrointestinal environment adaptation and probiotic properties, including acidic and bile stress tolerance, anti-inflammation, CAZymes, and utilization and biosynthesis of carbohydrate compounds, were identified in both genomes. Comparative genome analysis of the two genomes and 17 available complete L. johnsonii genomes revealed 101 genes specifically harbored by strains N5 and N7, several of which were implicated in potential probiotic properties. Overall, this study provides novel insights into the genetic basis of niche adaptation and probiotic properties, as well as the genome diversity of L. johnsonii. Full article
(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota, 2nd Edition)
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Review

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13 pages, 857 KiB  
Review
Transmission and Persistence of Infant Gut-Associated Bifidobacteria
by Margaret A. Hilliard and David A. Sela
Microorganisms 2024, 12(5), 879; https://doi.org/10.3390/microorganisms12050879 - 27 Apr 2024
Cited by 2 | Viewed by 3297
Abstract
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from [...] Read more.
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life. Full article
(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota, 2nd Edition)
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