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Advanced Research of Gut Microbiota in Health and Diseases

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A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 23188

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Dr. Andrea Piccioni

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Emergency Medicine Department, University Polyclinic Foundation A. Gemelli, IRCCS (Scientific Institute for Hospitalization and Treatment), 00168 Rome, Italy
Interests: Microbiota; Gut; Dysbiosis; Gut microbiome; Pathological conditions; Metabolic disorders; Autoimmune disease; Inflammatory disorders; Degenerative disease; Biomarkers; Sepsis; Emergency
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Dr. Federico Rosa

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Department of Emergency Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
Interests: Microbiota; Gut; Dysbiosis; Gut microbiome; Pathological conditions; Metabolic disorders; Autoimmune disease; Inflammatory disorders; Degenerative disease; Biomarkers; Sepsis; Emergency
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

One of the most interesting fields of research is that concerning gut microbiota.

The human gut microbiota can be considered an organ in its own right, with the peculiar characteristic of developing its basic features from the earliest years of life.

The study of the human microbiota is proving to be of fundamental importance in understanding the development and pathogenesis of numerous pathological conditions, not only of a gastroenterological nature.

Numerous pieces of evidence are highlighting a connection between dysregulation of the gut microbiota and the occurrence of numerous pathological conditions such as inflammatory and metabolic disorders, and degenerative and autoimmune diseases.

More and more works are highlighting the correlation between gut microbiota and disease occurrence, so it is of paramount importance to stay up-to-date with the latest evidence.

This Special Issue titled “Advanced research of gut microbiota in health and diseases” invites research and papers concerning the connection between alterations in the microbiota and the development of diseases affecting the digestive system and beyond.

Authors are also invited to participate with papers regarding the latest evidence on the state of the microbiota in the healthy individual, another of the most interesting and evolving topics.

Dr. Andrea Piccioni
Dr. Federico Rosa
Guest Editors

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Keywords

Microbiota
Gut
Dysbiosis
Gut microbiome
Pathological conditions
Metabolic disorders
Autoimmune disease
Inflammatory disorders
Degenerative diseases

Related Special Issue

Advanced Research of Gut Microbiota in Health and Diseases—2nd Edition in Biomedicines

Published Papers (11 papers)

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Research

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19 pages, 3274 KiB

Open AccessArticle

Gut Microbiota Signatures with Potential Clinical Usefulness in Colorectal and Non-Small Cell Lung Cancers

by Sofía Tesolato, Juan Vicente-Valor, Mateo Paz-Cabezas, Dulcenombre Gómez-Garre, Silvia Sánchez-González, Adriana Ortega-Hernández, Sofía de la Serna, Inmaculada Domínguez-Serrano, Jana Dziakova, Daniel Rivera, Jose-Ramón Jarabo, Ana-María Gómez-Martínez, Florentino Hernando, Antonio Torres and Pilar Iniesta

Biomedicines 2024, 12(3), 703; https://doi.org/10.3390/biomedicines12030703 - 21 Mar 2024

Viewed by 737

Abstract

The application of bacterial metagenomic analysis as a biomarker for cancer detection is emerging. Our aim was to discover gut microbiota signatures with potential utility in the diagnosis of colorectal cancer (CRC) and non-small cell lung cancer (NSCLC). A prospective study was performed on a total of 77 fecal samples from CRC and NSCLC patients and controls. DNA from stool was analyzed for bacterial genomic sequencing using the Ion Torrent™ technology. Bioinformatic analysis was performed using the QIIME2 pipeline. We applied logistic regression to adjust for differences attributable to sex, age, and body mass index, and the diagnostic accuracy of our gut signatures was compared with other previously published results. The feces of patients affected by different tumor types, such as CRC and NSCLC, showed a differential intestinal microbiota profile. After adjusting for confounders, Parvimonas (OR = 53.3), Gemella (OR = 6.01), Eisenbergiella (OR = 5.35), Peptostreptococcus (OR = 9.42), Lactobacillus (OR = 6.72), Salmonella (OR = 5.44), and Fusobacterium (OR = 78.9) remained significantly associated with the risk of CRC. Two genera from the Ruminococcaceae family, DTU089 (OR = 20.1) and an uncharacterized genus (OR = 160.1), were associated with the risk of NSCLC. Our two panels had better diagnostic capacity for CRC (AUC = 0.840) and NSLC (AUC = 0.747) compared to the application of two other published panels to our population. Thus, we propose a gut bacteria panel for each cancer type and show its potential application in cancer diagnosis. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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14 pages, 2448 KiB

Open AccessArticle

An Investigation of Metabolic Risk Factors and Gut Microbiota in Unexplained Syncope

by Susanna Longo, Federica Del Chierico, Matteo Scanu, Francesca Toto, Jacopo M. Legramante, Stefano Rizza, Lorenza Putignani and Massimo Federici

Biomedicines 2024, 12(2), 264; https://doi.org/10.3390/biomedicines12020264 - 24 Jan 2024

Viewed by 682

Abstract

Background: The pathogenesis of many syncopal episodes remains unexplained. Intestinal dysbiosis could be involved in the pathophysiological mechanisms of syncope due to its connection with the central nervous system via the microbiota–gut–brain axis. This pilot study aimed to explore the specific cardiometabolic risk factors and gut microbiota in unexplained syncope (US), compared to other types of syncope, to assess their similarity or verify their different origins. Methods: We studied 86 participants with syncope, who were divided into four groups: an orthostatic syncope group (OH, n = 24), a neuromediated syncope group (NMS, n = 26), a cardiological syncope group (CS, n = 9), and an unexplained syncope group (US, n = 27). We evaluated the anthropometric, clinical, and metabolic characteristics of the four groups; the α- and β-diversity; and the differences in the abundance of the microbial taxa. Results: The US group had a lower incidence of systolic hypertension at the first visit and a lower frequency of patients with nocturnal hypertension than the CS group. Compared to the OH and NMS groups, the US group had a higher incidence of carotid plaques and greater carotid intima–media thickness, respectively. The microbiota differed significantly between the US and CS groups, but not between the US group and the OH or NMS group. Conclusions: We observed significant differences in the gut microbiota between CS and US. Future studies are necessary to evaluate the involvement of the gut microbiota in the complex pathogenesis of syncope and whether its analysis could support the interpretation of the pathophysiological mechasnisms underlying some episodes classifiable as US. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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14 pages, 2741 KiB

Open AccessArticle

Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight

by Elio López-García, Antonio Benítez-Cabello, Antonio Pablo Arenas-de Larriva, Francisco Miguel Gutierrez-Mariscal, Pablo Pérez-Martínez, Elena María Yubero-Serrano, Francisco Noé Arroyo-López and Antonio Garrido-Fernández

Biomedicines 2023, 11(8), 2134; https://doi.org/10.3390/biomedicines11082134 - 28 Jul 2023

Viewed by 906

Abstract

This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer’s sex (male or female), age (19–46 years), and weight (48.6–99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers’ age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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15 pages, 3146 KiB

Open AccessArticle

Effects of Taurine on Gut Microbiota Homeostasis: An Evaluation Based on Two Models of Gut Dysbiosis

by Weike Qian, Mingyang Li, Leilei Yu, Fengwei Tian, Jianxin Zhao and Qixiao Zhai

Biomedicines 2023, 11(4), 1048; https://doi.org/10.3390/biomedicines11041048 - 29 Mar 2023

Cited by 7 | Viewed by 4841

Abstract

Taurine, an abundant free amino acid, plays multiple roles in the body, including bile acid conjugation, osmoregulation, oxidative stress, and inflammation prevention. Although the relationship between taurine and the gut has been briefly described, the effects of taurine on the reconstitution of intestinal flora homeostasis under conditions of gut dysbiosis and underlying mechanisms remain unclear. This study examined the effects of taurine on the intestinal flora and homeostasis of healthy mice and mice with dysbiosis caused by antibiotic treatment and pathogenic bacterial infections. The results showed that taurine supplementation could significantly regulate intestinal microflora, alter fecal bile acid composition, reverse the decrease in Lactobacillus abundance, boost intestinal immunity in response to antibiotic exposure, resist colonization by Citrobacter rodentium, and enhance the diversity of flora during infection. Our results indicate that taurine has the potential to shape the gut microbiota of mice and positively affect the restoration of intestinal homeostasis. Thus, taurine can be utilized as a targeted regulator to re-establish a normal microenvironment and to treat or prevent gut dysbiosis. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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12 pages, 1028 KiB

Open AccessArticle

In Vitro Evaluation of the Most Active Probiotic Strains Able to Improve the Intestinal Barrier Functions and to Prevent Inflammatory Diseases of the Gastrointestinal System

by Alessandra Fusco, Vittoria Savio, Donatella Cimini, Sergio D’Ambrosio, Adriana Chiaromonte, Chiara Schiraldi and Giovanna Donnarumma

Biomedicines 2023, 11(3), 865; https://doi.org/10.3390/biomedicines11030865 - 12 Mar 2023

Cited by 10 | Viewed by 1778

Abstract

Background: The integrity of the intestinal barrier is fundamental to gut health and homeostasis; its damage can increase intestinal permeability, with translocation of bacteria and/or endotoxins from gut, and the onset of various intestinal diseases. Lactobacillus spp. is one of the most common probiotics normally found in fermented foods and dairy products and is known for its anti-inflammatory and immunomodulatory properties and for its ability to protect and enhance the intestinal barrier functions. The aim of this work was to evaluate the ability of different strains of Lactobacillus spp. to improve in vitro the integrity of the intestinal barrier, to exert anti-inflammatory and immunomodulatory activity and to prevent Salmonella Typhimurium and enteroinvasive Escherichia coli (EIEC) infections. Methods: We analyzed the cellular expression of tight junctions, antimicrobial peptide HBD-2, pro-inflammatory cytokines and the inhibition of pathogens adhesion and invasion in a model of co-cultured epithelial cells treated with Lactobacillus spp. Results: L. brevis, L. reuteri and L. rhamnosus proved to be more effective in protecting the intestinal epithelium. Conclusions: These in vitro studies can help select strains particularly active in their intended use to obtain consortia formulations that can have as much maximum yield as possible in terms of patient benefit. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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16 pages, 4190 KiB

Open AccessArticle

Fecal Microbiota Transplantation Could Improve Chronic Diarrhea in Cynomolgus Monkey by Alleviating Inflammation and Modulating Gut Microbiota

by Puyuan Tian, Jiangmei Gao, Lifeng Liang, Bota Cui, Qiming Hu, Wenfeng Zhou, Bihai Li, Yiyan Liu, Tingtao Chen, Junhua Rao and Hong Wei

Biomedicines 2022, 10(12), 3016; https://doi.org/10.3390/biomedicines10123016 - 23 Nov 2022

Cited by 1 | Viewed by 1848

Abstract

Chronic diarrhea is associated with enteric dysbiosis and provokes the overuse of antibiotics. Fecal microbiota transplantation (FMT) is a promising therapy, but it shows discrepant clinical efficacy. Bacterial colonization in recipients has been studied, although little is known about the role of gut fungi and Archaea after FMT. In this study, we evaluated the efficacy of human-derived FMT on spontaneous chronic diarrhea cynomolgus monkeys and revealed the effector mechanisms. We demonstrated that FMT can mitigate the appearance of diarrheal symptoms and inhibit the increase in interleukin-6, interleukin-8, interleukin-1β, and interferon-γ and the decrease in interleukin-10 in serum. We confirmed that FMT restored the disturbance of gut bacteria by reducing the relative abundances of potential pathogens, including Cloacibacillus porcorum, Desulfovibrio desulfuricans, Erysipelotrichaceae bacterium 5_2_54FAA, and Erysipelotrichaceae bacterium 21_3, and increasing the levels of Lactobacillus fermentum and Lactobacillus ruminis CAG_367 in diarrheal monkeys. The metabolic pathways of healthy and FMT monkeys’ gut bacteria were enriched in amino acid metabolism, carbohydrate metabolism, and lipid metabolism, while the metabolic pathways of pre-FMT monkeys’ gut bacteria were enriched in antibiotic production. Moreover, a higher Ascomycota/Basidiomycota ratio, higher Aspergillus levels, and lower Trichosporon asahii abundance were present in intestinal fungi after FMT. Although the abundance of the Archaea Methanosphaera stastmanae did not change significantly, it was inversely correlated with the anti-inflammatory factor IL-4 after FMT. These results support the further development and application of FMT for chronic diarrhea. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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Review

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51 pages, 1067 KiB

Open AccessReview

From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes

by Frances Widjaja and Ivonne M. C. M. Rietjens

Biomedicines 2023, 11(10), 2658; https://doi.org/10.3390/biomedicines11102658 - 28 Sep 2023

Cited by 1 | Viewed by 1940

Abstract

The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine–feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either −20 °C for up to a few months or −80 °C for a longer period—up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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20 pages, 1827 KiB

Open AccessReview

Clinical Perspectives of Gut Microbiota in Patients with Chronic Kidney Disease and End-Stage Kidney Disease: Where Do We Stand?

by Alexandru Cosmin Pantazi, Mustafa Ali Kassim Kassim, Wassan Nori, Liliana Ana Tuta, Cristina Maria Mihai, Tatiana Chisnoiu, Adriana Luminita Balasa, Larisia Mihai, Ancuta Lupu, Corina Elena Frecus, Vasile Valeriu Lupu, Sergiu Ioachim Chirila, Anca Gabriela Badescu, Laurentiu-Tony Hangan and Simona Claudia Cambrea

Biomedicines 2023, 11(9), 2480; https://doi.org/10.3390/biomedicines11092480 - 07 Sep 2023

Cited by 6 | Viewed by 1708

Abstract

The gut microbiota (GM) plays a vital role in human health, with increasing evidence linking its imbalance to chronic kidney disease and end-stage kidney disease. Although the exact methods underlying kidney-GM crosstalk are not fully understood, interventions targeting GM were made and lay in three aspects: diagnostic, predictive, and therapeutic interventions. While these interventions show promising results in reducing uremic toxins and inflammation, challenges remain in the form of patient-specific GM variability, potential side effects, and safety concerns. Our understanding of GMs role in kidney disease is still evolving, necessitating further research to elucidate the causal relationship and mechanistic interactions. Personalized interventions focusing on specific GM signatures could enhance patient outcomes. However, comprehensive clinical trials are needed to validate these approaches’ safety, efficacy, and feasibility. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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14 pages, 305 KiB

Open AccessReview

Gut Microbiome in Patients after Heart Transplantation—Current State of Knowledge

by Katarzyna Olek, Agnieszka Anna Kuczaj, Szymon Warwas, Tomasz Hrapkowicz, Piotr Przybyłowski and Marta Tanasiewicz

Biomedicines 2023, 11(6), 1588; https://doi.org/10.3390/biomedicines11061588 - 30 May 2023

Cited by 1 | Viewed by 1267

Abstract

The human gut microbiota include over 10 trillion microorganisms, such as bacteria, fungi, viruses, archaea, and protozoa. Many reports indicate the strong correlation between dysbiosis and the severity of cardiovascular diseases. Microbiota seem to interact with the host’s alloimmunity and may have an immunomodulatory role in graft rejection processes. In our study, we present the current state of the knowledge of microbiota in heart transplant recipients. We present up-to-date microbiota diagnostic methods, interactions between microbiota and immunosuppressive drugs, the immunomodulatory effects of dysbiosis, and the available strategies (experimental and clinical strategies) to modulate host microbiota. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

21 pages, 1062 KiB

Open AccessReview

The Impact of Smoking on Microbiota: A Narrative Review

by Sara Cicchinelli, Federico Rosa, Federica Manca, Christian Zanza, Veronica Ojetti, Marcello Covino, Marcello Candelli, Antonio Gasbarrini, Francesco Franceschi and Andrea Piccioni

Biomedicines 2023, 11(4), 1144; https://doi.org/10.3390/biomedicines11041144 - 10 Apr 2023

Cited by 5 | Viewed by 3209

Abstract

Cigarette smoke is a classic risk factor for many diseases. The microbiota has been recently indicated as a new, major player in human health. Its deregulation—dysbiosis—is considered a new risk factor for several illnesses. Some studies highlight a cross-interaction between these two risk factors—smoke and dysbiosis—that may explain the pathogenesis of some diseases. We searched the keywords “smoking OR smoke AND microbiota” in the title of articles on PubMed^®, UptoDate^®, and Cochrane^®. We included articles published in English over the last 25 years. We collected approximately 70 articles, grouped into four topics: oral cavity, airways, gut, and other organs. Smoke may impair microbiota homeostasis through the same harmful mechanisms exerted on the host cells. Surprisingly, dysbiosis and its consequences affect not only those organs that are in direct contact with the smoke, such as the oral cavity or the airways, but also involve distant organs, such as the gut, heart, vessels, and genitourinary tract. These observations yield a deeper insight into the mechanisms implicated in the pathogenesis of smoke-related diseases, suggesting a role of dysbiosis. We speculate that modulation of the microbiota may help prevent and treat some of these illnesses. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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13 pages, 560 KiB

Open AccessReview

Pancreatic Cancer Resistance to Treatment: The Role of Microbiota

by Enrico Celestino Nista, Angelo Del Gaudio, Livio Enrico Del Vecchio, Teresa Mezza, Giulia Pignataro, Andrea Piccioni, Antonio Gasbarrini, Francesco Franceschi and Marcello Candelli

Biomedicines 2023, 11(1), 157; https://doi.org/10.3390/biomedicines11010157 - 07 Jan 2023

Cited by 5 | Viewed by 2562

Abstract

Pancreatic cancer (PC) is an aggressive malignancy and the fourth leading cause of cancer death in the United States and Europe. It is estimated that PC will be the second leading cause of cancer death by 2030. In addition to late diagnosis, treatment resistance is a major cause of shortened survival in pancreatic cancer. In this context, there is growing evidence that microbes play a regulatory role, particularly in therapy resistance and in creating a microenvironment in the tumor, that favors cancer progression. The presence of certain bacteria belonging to the gamma-proteobacteria or mycoplasmas appears to be associated with both pharmacokinetic and pharmacodynamic changes. Recent evidence suggests that the microbiota may also play a role in resistance mechanisms to immunotherapy and radiotherapy. However, the interactions between microbiota and therapy are bilateral and modulate therapy tolerance. Future perspectives are increasingly focused on elucidating the role of the microbiota in tumorigenesis and processes of therapy resistance, and a better understanding of these mechanisms may provide important opportunities to improve survival in these patients. Full article

(This article belongs to the Special Issue Advanced Research of Gut Microbiota in Health and Diseases)

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