High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota

Topic Information

Dear Colleagues,

The advent of high-throughput technologies has significantly contributed to expanding our knowledge on the composition of the resident microbiota of different human niches, including the gut, skin, and genital tract, in health as well as disease conditions. In this regard, in recent years, the microbiota has been involved in several pathologies, such as bacterial as well as viral infections (e.g., Chlamydia trachomatis and/or HPV in the female genital tract) or chronic inflammatory conditions (e.g., diabetes, obesity, chronic atrophic gastritis or non-atrophic pangastritis). The growing body of data provided by the different approaches for microbiota investigation, such as DNA sequences from next-generation sequencing techniques, can be analyzed via several powerful computational methods to provide a comprehensive description of the bacterial composition as well as a functional characterization via the prediction of metabolic pathways. In the present topic collection, we welcome innovative articles on the interrelationship between the different microbial communities and the pathophysiology of human diseases. We are interested in full-length manuscripts based on original research, systematic reviews and/or meta-analyses, and methodological advances.

Dr. Simone Filardo
Dr. Rosa Sessa
Prof. Andrea Carolina Entrocassi
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Gastroenterology Insights gastroent	1.5	2.8	2009	34 Days	CHF 1600
Infectious Disease Reports idr	3.4	5.1	2009	32.4 Days	CHF 1800
Life life	3.2	4.3	2011	17.8 Days	CHF 2600
Microbiology Research microbiolres	2.1	1.9	2010	15.4 Days	CHF 1600
Microorganisms microorganisms	4.1	7.4	2013	11.7 Days	CHF 2700

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Published Papers (6 papers)

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14 pages, 1846 KiB  

Open AccessArticle

Gut Microbiome Profiles in Colorectal Cancer Patients in Iraq

by Fatima J. Kadhim, Zahid S. Aziz and Khalid S. Ibrahim

Microbiol. Res. 2025, 16(1), 22; https://doi.org/10.3390/microbiolres16010022 - 16 Jan 2025

Viewed by 1225

Abstract

Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally, and is a significant contributor to both morbidity and mortality rates. Emerging research has promptly highlighted the potential role of the gut microbiome in the development and progression of CRC. This study [...] Read more.

Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally, and is a significant contributor to both morbidity and mortality rates. Emerging research has promptly highlighted the potential role of the gut microbiome in the development and progression of CRC. This study aims to investigate the differences in gut microbiota between CRC patients and healthy individuals in Iraq, using 16S rRNA metagenomic sequencing on Illumina NovaSeq (PE250-Seq). A total of 21 stool samples were analyzed: 12 from early-stage CRC patients and nine from healthy controls. Bacterial DNA was extracted, followed by 16S rRNA amplicon sequencing to profile the microbial communities. The results indicated significant differences between the fecal microbiome of the two groups. Remarkably, CRC patients exhibited a marked reduction in Bacteroidota and an increase in Verrucomicrobiota compared to healthy controls. At the genus level, Prevotella, Faecalibacterium, Roseburia, Barnesiella, Eubacterium Lachnospiraceae_UCG_004, and Lachnospira were significantly less abundant in CRC patients compared to the healthy individuals, while Actinomyces, Monoglobus, Desulfovibrio, Akkermansia, and Bacteroides were highly enriched. In addition, diversity analyses further indicated decreased α-diversity and distinct β-diversity patterns in the CRC patients, suggesting significant shifts in the gut microbial composition. These findings underscore the potential of microbiome-based diagnostics and therapeutic strategies, with microbial alterations serving as biomarkers for CRC diagnosis. Further research needs to focus on elucidating the causal relationships and therapeutic potential of these microbiome changes in CRC management. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

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13 pages, 3319 KiB  

Open AccessArticle

Impact of Environmental pH on the Structure and Diversity of Oral Microbiota: An In Vitro Study

by Yao Huang, Takayuki Nambu, Hiroki Takigawa, Akiyo Kawamoto, Toshinori Okinaga and Kazuya Takahashi

Microbiol. Res. 2024, 15(4), 2764-2776; https://doi.org/10.3390/microbiolres15040183 - 23 Dec 2024

Viewed by 1124

Abstract

Although in vivo studies have explored the relationship between oral environment and microbial communities, a precise analysis of the effects of environmental pH on oral microbiota remains challenging owing to their complexity and external influences. This study aimed to investigate the effect of [...] Read more.

Although in vivo studies have explored the relationship between oral environment and microbial communities, a precise analysis of the effects of environmental pH on oral microbiota remains challenging owing to their complexity and external influences. This study aimed to investigate the effect of environmental pH on the structure and diversity of oral microbiota in vitro. Tongue coating samples from ten participants were cultured anaerobically at six pH levels (5.5–8.0) using adjusted media. After DNA extraction, high-throughput sequencing of the 16s rRNA V3–V4 region was performed. Microbial diversity was analyzed using alpha and beta diversity indices, and differential taxa were identified using linear discriminant analysis effect size (LEfSe). Alpha diversity analysis revealed reduced diversity at pH 5.5 and 8.0. Beta diversity revealed that microbial communities at pH 5.5, 7.5, and 8.0 were separated from those at pH 7.0. LEfSe identified bacterial species that were significantly altered at pH 5.5 and 8.0. Environmental pH significantly influences the diversity and composition of microbial communities, with substantial changes occurring under acidic or alkaline conditions. These findings provide deeper insight into how oral biofilms respond to pH variations, underscoring the critical role of pH in oral microbiota dynamics. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

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18 pages, 910 KiB  

Open AccessReview

Microbiota and Recurrent Pregnancy Loss (RPL); More than a Simple Connection

by Jenny Valentina Garmendia, Claudia Valentina De Sanctis, Marián Hajdúch and Juan Bautista De Sanctis

Microorganisms 2024, 12(8), 1641; https://doi.org/10.3390/microorganisms12081641 - 10 Aug 2024

Cited by 3 | Viewed by 2989

Abstract

Recurrent Pregnancy Loss (RPL) affects 1–2% of women, and its triggering factors are unclear. Several studies have shown that the vaginal, endometrial, and gut microbiota may play a role in RPL. A decrease in the quantity of Lactobacillus crispatus in local microbiota has [...] Read more.

Recurrent Pregnancy Loss (RPL) affects 1–2% of women, and its triggering factors are unclear. Several studies have shown that the vaginal, endometrial, and gut microbiota may play a role in RPL. A decrease in the quantity of Lactobacillus crispatus in local microbiota has been associated with an increase in local (vaginal and endometrial) inflammatory response and immune cell activation that leads to pregnancy loss. The inflammatory response may be triggered by gram-negative bacteria, lipopolysaccharides (LPS), viral infections, mycosis, or atypia (tumor growth). Bacterial structures and metabolites produced by microbiota could be involved in immune cell modulation and may be responsible for immune cell activation and molecular mimicry. Gut microbiota metabolic products may increase the amount of circulating pro-inflammatory lymphocytes, which, in turn, will migrate into vaginal or endometrial tissues. Local pro-inflammatory Th1 and Th17 subpopulations and a decrease in local Treg and tolerogenic NK cells are accountable for the increase in pregnancy loss. Local microbiota may modulate the local inflammatory response, increasing pregnancy success. Analyzing local and gut microbiota may be necessary to characterize some RPL patients. Although oral supplementation of probiotics has not been shown to modify vaginal or endometrial microbiota, the metabolites produced by it may benefit patients. Lactobacillus crispatus transplantation into the vagina may enhance the required immune tolerogenic response to achieve a normal pregnancy. The effect of hormone stimulation and progesterone to maintain early pregnancy on microbiota has not been adequately studied, and more research is needed in this area. Well-designed clinical trials are required to ascertain the benefit of microbiota modulation in RPL. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

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13 pages, 1298 KiB  

Open AccessCommunication

Comparative Genomics of Three Hybrid-Pathogen Multidrug-Resistant Escherichia coli Strains Isolated from Healthy Donors’ Feces

by Judith Z. Ortega-Enríquez, Claudia Martínez-de la Peña, Cristina Lara-Ochoa, Rosa del Carmen Rocha-Gracia, Edwin Barrios-Villa and Margarita M. P. Arenas-Hernández

Microbiol. Res. 2024, 15(3), 1412-1424; https://doi.org/10.3390/microbiolres15030095 - 2 Aug 2024

Viewed by 2253

Abstract

The present study shows the genomic characterization of three pathogenic Escherichia coli hybrid strains. All strains were previously characterized as diarrheagenic pathotypes (DEC), obtained from feces. The three sequenced strains have genes that encode adhesins (fimH and iha) and iron uptake [...] Read more.

The present study shows the genomic characterization of three pathogenic Escherichia coli hybrid strains. All strains were previously characterized as diarrheagenic pathotypes (DEC), obtained from feces. The three sequenced strains have genes that encode adhesins (fimH and iha) and iron uptake systems (iucC and iutA). Antibiotic resistance genes were also found for fluoroquinolone and aminoglycoside families in the three strains. The presence of genomic islands (GIs) in the sequenced study strains presented 100% identity (Ec-25.2) and 99% identity (Ec-36.1) with previously reported Extraintestinal Pathogenic E. coli (ExPEC) strains. The Ec-36.4 strain shared a 99% identity with GI from the Enterotoxigenic E. coli (ETEC) pathotype of the diarrheagenic E. coli strain. Ec-25.2 belongs to ST69 and harbors a FimH27 variant, while Ec-36.1 and Ec-36.4 belong to ST4238 and share a FimH54 variant. Four incompatibility groups associated with conjugative plasmids were identified (IncFIB, IncF11, IncI1, and IncB/O/K/Z), as well as Insertion Sequences and MITEs elements. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

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15 pages, 2571 KiB  

Open AccessArticle

Sequential Sampling of the Gastrointestinal Tract to Characterize the Entire Digestive Microbiome in Japanese Subjects

by Kota Ishizawa, Toru Tamahara, Suguo Suzuki, Yutaka Hatayama, Bin Li, Michiaki Abe, Yuichi Aoki, Ryutaro Arita, Natsumi Saito, Minoru Ohsawa, Soichiro Kaneko, Rie Ono, Shin Takayama, Muneaki Shimada, Kazuki Kumada, Tomoyuki Koike, Atsushi Masamune, Ko Onodera, Tadashi Ishii, Ritsuko Shimizu and Takeshi Kannoadd Show full author list remove Hide full author list

Microorganisms 2024, 12(7), 1324; https://doi.org/10.3390/microorganisms12071324 - 28 Jun 2024

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Abstract

The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive [...] Read more.

The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive metagenomic datasets covering the entire tract are scarce due to cost and technical challenges. Despite the widespread use of fecal samples, integrated datasets encompassing the entire digestive process, beginning at the mouth and ending with feces, are lacking. With this study, we aimed to fill this gap by analyzing the complete metagenome of the GI tract, providing insights into the dynamics of the microbiota and potential therapeutic avenues. In this study, we delved into the complex world of the GI microbiota, which we examined in five healthy Japanese subjects. While samples from the whole GI flora and fecal samples provided sufficient bacteria, samples obtained from the stomach and duodenum posed a challenge. Using a principal coordinate analysis (PCoA), clear clustering patterns were identified; these revealed significant diversity in the duodenum. Although this study was limited by its small sample size, the flora in the overall GI tract showed unwavering consistency, while the duodenum exhibited unprecedented phylogenetic diversity. A visual heat map illustrates the discrepancy in abundance, with Fusobacteria and Bacilli dominating the upper GI tract and Clostridia and Bacteroidia dominating the fecal samples. Negativicutes and Actinobacteria were found throughout the digestive tract. This study demonstrates that it is possible to continuously collect microbiome samples throughout the human digestive tract. These findings not only shed light on the complexity of GI microbiota but also provide a basis for future research. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

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17 pages, 2431 KiB  

Open AccessArticle

Automated Protocol for Monitoring Droplets and Fomites on Surfaces

by Federica Valeriani, Lory Marika Margarucci, Francesca Ubaldi, Gianluca Gianfranceschi and Vincenzo Romano Spica

Microbiol. Res. 2024, 15(1), 120-136; https://doi.org/10.3390/microbiolres15010008 - 27 Dec 2023

Viewed by 1785

Abstract

During the COVID-19 pandemic, extensive efforts focused on developing a better understanding of indirect transmission routes, environmental monitoring of fomites, and suitable surveillance strategies, providing new perspectives to also face other communicable diseases. Rapid methods for monitoring environmental contamination are strongly needed to [...] Read more.

During the COVID-19 pandemic, extensive efforts focused on developing a better understanding of indirect transmission routes, environmental monitoring of fomites, and suitable surveillance strategies, providing new perspectives to also face other communicable diseases. Rapid methods for monitoring environmental contamination are strongly needed to support risk assessment, epidemiological surveillance and prevent infections from spreading. We optimized and automatized a protocol based on fomite detection by qPCR, using a microbial-signature approach based on marker genes belonging to the microbiota of droplets or different biological fluids. The procedure was implemented by exploiting the available tools developed for SARS-CoV-2 tracing, such as flocked swab sampling, real-time PCR equipment and automatic extraction of nucleic acids. This approach allowed scaling up, simplifying, and speeding up the extraction step of environmental swabs, processing at least 48 samples within 45 min vs. 90 min for about 24 samples by manual protocols. A comparison of microflora data by Next-Generation Sequencing (NGS) strongly supports the effectiveness of this semiautomated extraction procedure, providing good quality DNA with comparable representation of species as shown by biodiversity indexes. Today, equipment for qPCR is widely available and relatively inexpensive; therefore this approach may represent a promising tool for hospital hygiene in surveilling fomites associated with SARS-CoV-2 or other pathogen’s transmission. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

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