Editorial

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Open AccessEditorial

Special Issue “Gut Microbioma Structure and Functions in Human Health and Disease”: Editorial

by Francesco Di Pierro

Microorganisms 2023, 11(5), 1220; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11051220 - 06 May 2023

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The human gut microbiota is an integral component of the human body that can strike a delicate balance between health and disease [...] Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

Research

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19 pages, 3277 KiB

Open AccessArticle

Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d’Ivoire

by Veronica Di Cristanziano, Fedja Farowski, Federica Berrilli, Maristella Santoro, David Di Cave, Christophe Glé, Martin Daeumer, Alexander Thielen, Maike Wirtz, Rolf Kaiser, Kirsten Alexandra Eberhardt, Maria J. G. T. Vehreschild and Rossella D’Alfonso

Microorganisms 2021, 9(8), 1763; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081763 - 18 Aug 2021

Cited by 7 | Viewed by 2542

Abstract

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition [...] Read more.

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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11 pages, 6348 KiB

Open AccessArticle

Differences in the On- and Off-Tumor Microbiota between Right- and Left-Sided Colorectal Cancer

by Oliver Phipps, Mohammed N. Quraishi, Edward A. Dickson, Helen Steed, Aditi Kumar, Austin G. Acheson, Andrew D. Beggs, Matthew J. Brookes and Hafid Omar Al-Hassi

Microorganisms 2021, 9(5), 1108; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051108 - 20 May 2021

Cited by 16 | Viewed by 5163

Abstract

This study aims to determine differences in the on- and off-tumor microbiota between patients with right- and left-sided colorectal cancer. Microbiome profiling of tumor and tumor-adjacent biopsies from patients with right-sided (n = 17) and left-sided (n = 7) colorectal adenocarcinoma [...] Read more.

This study aims to determine differences in the on- and off-tumor microbiota between patients with right- and left-sided colorectal cancer. Microbiome profiling of tumor and tumor-adjacent biopsies from patients with right-sided (n = 17) and left-sided (n = 7) colorectal adenocarcinoma was performed using 16S ribosomal RNA sequencing. Off-tumor alpha and beta diversity were significantly different between right- and left-sided colorectal cancer patients. However, no differences in on-tumor diversity were observed between tumor locations. Comparing the off-tumor microbiota showed the right colon to be enriched with species of the Lachnoclostridium, Selenomonas, and Ruminococcus genera. Whereas the left colon is enriched with Epsilonbacteraeota phylum, Campylobacteria class, and Pasteurellales and Campylobacterales orders, in contrast, the on-tumor microbiota showed relatively fewer differences in bacterial taxonomy between tumor sites, with left tumors being enriched with Methylophilaceae and Vadin BE97 families and Alloprevotella, Intestinibacter, Romboutsia, and Ruminococcus 2 genera. Patients with left-sided colorectal cancer had large taxonomic differences between their paired on- and off-tumor microbiota, while patients with right-sided colorectal cancer showed relatively fewer taxonomic differences. Collectively, this suggests that the right and left colon show distinctive bacterial populations; however, the presence of a colonic tumor leads to a more consistent microbiota between locations. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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16 pages, 1992 KiB

Open AccessArticle

Oral Microbiota of Children Is Conserved across Han, Tibetan and Hui Groups and Is Correlated with Diet and Gut Microbiota

by Ke Liu, Siyu Chen, Jing Huang, Feihong Ren, Tingyu Yang, Danfeng Long, Huan Li and Xiaodan Huang

Microorganisms 2021, 9(5), 1030; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051030 - 11 May 2021

Cited by 9 | Viewed by 2383

Abstract

The oral microbiota can be affected by several factors; however, little is known about the relationship between diet, ethnicity and commensal oral microbiota among school children living in close geographic proximity. In addition, the relationship between the oral and gut microbiota remains unclear. [...] Read more.

The oral microbiota can be affected by several factors; however, little is known about the relationship between diet, ethnicity and commensal oral microbiota among school children living in close geographic proximity. In addition, the relationship between the oral and gut microbiota remains unclear. We collected saliva from 60 school children from the Tibetan, Han and Hui ethnicities for a 16S rRNA gene sequencing analysis and comparison with previously collected fecal samples. The study revealed that Bacteroidetes and Proteobacteria were the dominant phyla in the oral microbiota. The Shannon diversity was lowest in the Tibetan group. A PCA showed a substantial overlap in the distribution of the taxa, indicating a high degree of conservation among the oral microbiota across ethnic groups while the enrichment of a few specific taxa was observed across different ethnic groups. The consumption of seafood, poultry, sweets and vegetables was significantly correlated with multiple oral microbiotas. Furthermore, 123 oral genera were significantly associated with 191 gut genera. A principal coordinate analysis revealed that the oral microbiota clustered separately from the gut microbiota. This work extends the findings of previous studies comparing microbiota from human populations and provides a basis for the exploration of the interactions governing the tri-partite relationship between diet, oral microbiota and gut microbiota. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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18 pages, 611 KiB

Open AccessArticle

Gut Microbiome of a Multiethnic Community Possessed No Predominant Microbiota

by Wei Wei Thwe Khine, Anna Hui Ting Teo, Lucas Wee Wei Loong, Jarett Jun Hao Tan, Clarabelle Geok Hui Ang, Winnie Ng, Chuen Neng Lee, Congju Zhu, Quek Choon Lau and Yuan-Kun Lee

Microorganisms 2021, 9(4), 702; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040702 - 29 Mar 2021

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Abstract

With increasing globalisation, various diets from around the world are readily available in global cities. This study aimed to verify if multiethnic dietary habits destabilised the gut microbiome in response to frequent changes, leading to readily colonisation of exogenous microbes. This may have [...] Read more.

With increasing globalisation, various diets from around the world are readily available in global cities. This study aimed to verify if multiethnic dietary habits destabilised the gut microbiome in response to frequent changes, leading to readily colonisation of exogenous microbes. This may have health implications. We profiled Singapore young adults of different ethnicities for dietary habits, faecal type, gut microbiome and cytokine levels. Subjects were challenged with Lactobacillus casei, and corresponding changes in microbiome and cytokines were evaluated. Here, we found that the majority of young adults had normal stool types (73% Bristol Scale Types 3 and 4) and faecal microbiome categorised into three clusters, irrespective of race and gender. Cluster 1 was dominated by Bacteroides, Cluster 2 by Prevotella, while Cluster 3 showed a marginal increase in Blautia, Ruminococaceae and Ruminococcus, without a predominant microbiota. These youngsters in the three faecal microbiome clusters preferred Western high sugary beverages, Southeast Asian plant-rich diet and Asian/Western diets in rotation, respectively. Multiethnic dietary habits (Cluster 3) led to a gut microbiome without predominant microbiota yet demonstrated colonisation resistance to Lactobacillus. Although Bacteroides and Prevotella are reported to be health-promoting but also risk factors for some illnesses, Singapore-style dietary rotation habits may alleviate Bacteroides and Prevotella associated ill effects. Different immunological outcome was observed during consumption of the lactobacilli among the three microbiome clusters. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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Review

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19 pages, 1724 KiB

Open AccessReview

The Potential Utility of Prebiotics to Modulate Alzheimer’s Disease: A Review of the Evidence

by Jea Woo Kang and Angela M. Zivkovic

Microorganisms 2021, 9(11), 2310; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112310 - 06 Nov 2021

Cited by 14 | Viewed by 7089

Abstract

The gut microbiome has recently emerged as a critical modulator of brain function, with the so-called gut-brain axis having multiple links with a variety of neurodegenerative and mental health conditions, including Alzheimer’s Disease (AD). Various approaches for modulating the gut microbiome toward compositional [...] Read more.

The gut microbiome has recently emerged as a critical modulator of brain function, with the so-called gut-brain axis having multiple links with a variety of neurodegenerative and mental health conditions, including Alzheimer’s Disease (AD). Various approaches for modulating the gut microbiome toward compositional and functional states that are consistent with improved cognitive health outcomes have been documented, including probiotics and prebiotics. While probiotics are live microorganisms that directly confer beneficial health effects, prebiotics are oligosaccharide and polysaccharide structures that can beneficially modulate the gut microbiome by enhancing the growth, survival, and/or function of gut microbes that in turn have beneficial effects on the human host. In this review, we discuss evidence showing the potential link between gut microbiome composition and AD onset or development, provide an overview of prebiotic types and their roles in altering gut microbial composition, discuss the effectiveness of prebiotics in regulating gut microbiome composition and microbially derived metabolites, and discuss the current evidence linking prebiotics with health outcomes related to AD in both animal models and human trials. Though there is a paucity of human clinical trials demonstrating the effectiveness of prebiotics in altering gut microbiome-mediated health outcomes in AD, current evidence highlights the potential of various prebiotic approaches for beneficially altering the gut microbiota or gut physiology by promoting the production of butyrate, indoles, and secondary bile acid profiles that further regulate gut immunity and mucosal homeostasis, which are associated with beneficial effects on the central immune system and brain functionality. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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16 pages, 1643 KiB

Open AccessReview

Gut Microbiota and Host Metabolism: From Proof of Concept to Therapeutic Intervention

by Patrice D. Cani, Emilie Moens de Hase and Matthias Van Hul

Microorganisms 2021, 9(6), 1302; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061302 - 15 Jun 2021

Cited by 46 | Viewed by 10686

Abstract

The field of the gut microbiota is still a relatively young science area, yet many studies have already highlighted the translational potential of microbiome research in the context of human health and disease. However, like in many new fields, discoveries are occurring at [...] Read more.

The field of the gut microbiota is still a relatively young science area, yet many studies have already highlighted the translational potential of microbiome research in the context of human health and disease. However, like in many new fields, discoveries are occurring at a fast pace and have provided new hope for the development of novel clinical applications in many different medical conditions, not in the least in metabolic disorders. This rapid progress has left the field vulnerable to premature claims, misconceptions and criticism, both from within and outside the sector. Tackling these issues requires a broad collaborative effort within the research field and is only possible by acknowledging the difficulties and challenges that are faced and that are currently hindering clinical implementation. These issues include: the primarily descriptive nature of evidence, methodological concerns, disagreements in analysis techniques, lack of causality, and a rather limited molecular-based understanding of underlying mechanisms. In this review, we discuss various studies and models that helped identifying the microbiota as an attractive tool or target for developing various translational applications. We also discuss some of the limitations and try to clarify some common misconceptions that are still prevalent in the field. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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Other

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13 pages, 1264 KiB

Open AccessSystematic Review

Evaluation of the Effect of Limosilactobacillus fermentum CECT5716 on Gastrointestinal Infections in Infants: A Systematic Review and Meta-Analysis

by Belén Pastor-Villaescusa, Ruth Blanco-Rojo and Mónica Olivares

Microorganisms 2021, 9(7), 1412; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071412 - 30 Jun 2021

Cited by 7 | Viewed by 2740

Abstract

Reducing the incidence of gastrointestinal infections (GIs) that occur at early stages to mitigate hospitalizations and treatments with adverse effects is a promising strategy for providing well-being to infants and their families. This systematic review and meta-analysis explores whether the early administration of [...] Read more.

Reducing the incidence of gastrointestinal infections (GIs) that occur at early stages to mitigate hospitalizations and treatments with adverse effects is a promising strategy for providing well-being to infants and their families. This systematic review and meta-analysis explores whether the early administration of Limosilactobacillus fermentum CECT5716 might be effective as a preventive therapy for GIs. We reviewed the literature to identify randomized controlled trials (RCTs) investigating the effectiveness of milk formulas supplemented with L. fermentum CECT5716 administered to infants at early stages to reduce the incidence of GIs. The MEDLINE (via PubMed), Web of Science (WoS), and Cochrane Central Register of Controlled Trials (via CENTRAL) databases were searched up to 15 June 2021. GI data from the included studies were synthesized in a random-effects model. Three RCTs were finally selected including 435 infants. There was a significant reduction in the incidence rate of GIs for those receiving L. fermentum CECT5716 compared with those receiving placebo (IRR: 0.52, 95% CI: 0.36–0.74, p = 0.0004). Heterogeneity between studies was moderate (I² = 54.5%). Based on the present systematic review and meta-analysis, the administration of L. fermentum CECT5716 at doses from 1 × 10⁹ to 8.4 × 10⁸ cfu/day in milk formulas may prevent GIs in infants up to 12 months old. Longer-term studies including a higher number of infants are needed to determine whether the use of this probiotic during the early stages of life is an efficient way to reduce the incidence of GIs. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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