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14 pages, 4471 KiB

Open AccessArticle

M-Batches to Simulate Luminal and Mucosal Human Gut Microbial Ecosystems: A Case Study of the Effects of Coffee and Green Tea

by Elizabeth Goya-Jorge, Irma Gonza, Caroline Douny, Marie-Louise Scippo and Véronique Delcenserie

Microorganisms 2024, 12(2), 236; https://doi.org/10.3390/microorganisms12020236 - 23 Jan 2024

Cited by 1 | Viewed by 1097

Abstract

Gastrointestinal simulations in vitro have only limited approaches to analyze the microbial communities inhabiting the mucosal compartment. Understanding and differentiating gut microbial ecosystems is crucial for a more comprehensive and accurate representation of the gut microbiome and its interactions with the host. Herein [...] Read more.

Gastrointestinal simulations in vitro have only limited approaches to analyze the microbial communities inhabiting the mucosal compartment. Understanding and differentiating gut microbial ecosystems is crucial for a more comprehensive and accurate representation of the gut microbiome and its interactions with the host. Herein is suggested, in a short-term and static set-up (named “M-batches”), the analysis of mucosal and luminal populations of inhabitants of the human colon. After varying several parameters, such as the fermentation volume and the fecal inoculum (single or pool), only minor differences in microbial composition and metabolic production were identified. However, the pool created with feces from five donors and cultivated in a smaller volume (300 mL) seemed to provide a more stable luminal ecosystem. The study of commercially available coffee and green tea in the M-batches suggested some positive effects of these worldwide known beverages, including the increase in butyrate-producing bacteria and lactobacilli populations. We hope that this novel strategy can contribute to future advances in the study of intestinal ecosystems and host-microbe relationships and help elucidate roles of the microbiome in health and disease. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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15 pages, 4163 KiB

Open AccessArticle

Individual and Group-Based Effects of In Vitro Fiber Interventions on the Fecal Microbiota

by Valeria Agamennone, Tim J. van den Broek, Alie de Kat Angelino-Bart, Femke P. M. Hoevenaars, Jan Willem van der Kamp and Frank H. J. Schuren

Microorganisms 2023, 11(8), 2001; https://doi.org/10.3390/microorganisms11082001 - 03 Aug 2023

Cited by 1 | Viewed by 1061

Abstract

The development of microbiome-targeted strategies is limited by individual differences in gut microbiome composition and metabolic responses to interventions. In vitro models that can replicate this variation allow us to conduct pre-clinical studies and assess efficacy. This study describes the exposure of 16 [...] Read more.

The development of microbiome-targeted strategies is limited by individual differences in gut microbiome composition and metabolic responses to interventions. In vitro models that can replicate this variation allow us to conduct pre-clinical studies and assess efficacy. This study describes the exposure of 16 individual fecal microbiota samples to 5 different fibers using an in vitro system for the anaerobic cultivation of bacteria. The individual microbiota differed in composition and metabolite profiles (short-chain fatty acids and branched-chain fatty acids) after incubation with the fibers. Furthermore, microbiota composition after fiber incubation was significantly different between subjects with good intestinal health and subjects with Inflammatory Bowel Disease (IBD). α-diversity was differently affected by dietary fibers; for example, exposure to psyllium resulted in increased diversity in the healthy group and in decreased diversity in the IBD group. Instead, the functional metabolic profile did not differ between the two groups. Finally, the combination of all fibers, tested on the microbiota from IBD subjects, resulted in stronger overall effects on both microbiota composition and metabolite production compared to the single fibers. These results confirm that incubation with dietary fiber results in different compositional and functional effects on individual microbiota and that in vitro models represent successful tools for studying individual fiber effects. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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15 pages, 3097 KiB

Open AccessArticle

Gut Protective Effect from Newly Isolated Bacteria as Probiotics against Dextran Sulfate Sodium and Carrageenan-Induced Ulcerative Colitis

by Yuka Ikeda, Ai Tsuji and Satoru Matsuda

Microorganisms 2023, 11(7), 1858; https://doi.org/10.3390/microorganisms11071858 - 23 Jul 2023

Viewed by 1371

Abstract

Gut microbiome dysbiosis might be linked to certain diseases such as inflammatory bowel diseases (IBDs), which are categorized by vigorous inflammation of the gastrointestinal tract. Several studies have shown the favorable anti-inflammatory effect of certain probiotics in IBD therapy. In the present investigation, [...] Read more.

Gut microbiome dysbiosis might be linked to certain diseases such as inflammatory bowel diseases (IBDs), which are categorized by vigorous inflammation of the gastrointestinal tract. Several studies have shown the favorable anti-inflammatory effect of certain probiotics in IBD therapy. In the present investigation, the possible gut protective effects of commensal bacteria were examined in an IBD model mouse that was cost-effectively induced with low molecular weight dextran sulfate sodium (DSS) and kappa carrageenan. Our conclusions show that certain probiotic supplementation could result in the attenuation of the disease condition in the IBD mouse, suggesting a favorable therapeutic capability for considerably improving symptoms of gut inflammation with an impact on the IBD therapy. However, the molecular mechanisms require further investigation. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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12 pages, 2683 KiB

Open AccessArticle

Impact of Bacillus cereus on the Human Gut Microbiota in a 3D In Vitro Model

by Marco Calvigioni, Adelaide Panattoni, Francesco Biagini, Leonardo Donati, Diletta Mazzantini, Mariacristina Massimino, Costanza Daddi, Francesco Celandroni, Giovanni Vozzi and Emilia Ghelardi

Microorganisms 2023, 11(7), 1826; https://doi.org/10.3390/microorganisms11071826 - 17 Jul 2023

Cited by 1 | Viewed by 1247

Abstract

In vitro models for culturing complex microbial communities are progressively being used to study the effects of different factors on the modeling of in vitro-cultured microorganisms. In previous work, we validated a 3D in vitro model of the human gut microbiota based on [...] Read more.

In vitro models for culturing complex microbial communities are progressively being used to study the effects of different factors on the modeling of in vitro-cultured microorganisms. In previous work, we validated a 3D in vitro model of the human gut microbiota based on electrospun gelatin scaffolds covered with mucins. The aim of this study was to evaluate the effect of Bacillus cereus, a pathogen responsible for food poisoning diseases in humans, on the gut microbiota grown in the model. Real-time quantitative PCR and 16S ribosomal RNA-gene sequencing were performed to obtain information on microbiota composition after introducing B. cereus ATCC 14579 vegetative cells or culture supernatants. The adhesion of B. cereus to intestinal mucins was also tested. The presence of B. cereus induced important modifications in the intestinal communities. Notably, levels of Proteobacteria (particularly Escherichia coli), Lactobacillus, and Akkermansia were reduced, while abundances of Bifidobacterium and Mitsuokella increased. In addition, B. cereus was able to adhere to mucins. The results obtained from our in vitro model stress the hypothesis that B. cereus is able to colonize the intestinal mucosa by stably adhering to mucins and impacting intestinal microbial communities as an additional pathogenetic mechanism during gastrointestinal infection. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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16 pages, 6370 KiB

Open AccessArticle

Metataxonomic Analysis Demonstrates a Shift in Duodenal Microbiota in Patients with Obstructive Jaundice

by Benjamin Hart, Jasmin Patel, Pieter De Maayer, Ekene Emmanuel Nweke and Damon Bizos

Microorganisms 2023, 11(6), 1611; https://doi.org/10.3390/microorganisms11061611 - 18 Jun 2023

Viewed by 1292

Abstract

The human gastrointestinal tract (GIT) is home to an abundance of diverse microorganisms, and the balance of this microbiome plays a vital role in maintaining a healthy GIT. The obstruction of the flow of bile into the duodenum, resulting in obstructive jaundice (OJ), [...] Read more.

The human gastrointestinal tract (GIT) is home to an abundance of diverse microorganisms, and the balance of this microbiome plays a vital role in maintaining a healthy GIT. The obstruction of the flow of bile into the duodenum, resulting in obstructive jaundice (OJ), has a major impact on the health of the affected individual. This study sought to identify changes in the duodenal microbiota in South African patients with OJ compared to those without this disorder. Mucosal biopsies were taken from the duodenum of nineteen jaundiced patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and nineteen control participants (non-jaundiced patients) undergoing gastroscopy. DNA extracted from the samples was subjected to 16S rRNA amplicon sequencing using the Ion S5 TM sequencing platform. Diversity metrics and statistical correlation analyses with the clinical data were performed to compare duodenal microbial communities in both groups. Differences in the mean distribution of the microbial communities in the jaundiced and non-jaundiced samples were observed; however, this difference did not reach statistical significance. Of note, there was a statistically significant difference between the mean distributions of bacteria comparing jaundiced patients with cholangitis to those without (p = 0.0026). On further subset analysis, a significant difference was observed between patients with benign (Cholelithiasis) and malignant disease, namely, head of pancreas (HOP) mass (p = 0.01). Beta diversity analyses further revealed a significant difference between patients with stone and non-stone related disease when factoring in the Campylobacter-Like Organisms (CLO) test status (p = 0.048). This study demonstrated a shift in the microbiota in jaundiced patients, especially considering some underlying conditions of the upper GI tract. Future studies should aim to verify these findings in a larger cohort. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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18 pages, 2961 KiB

Open AccessArticle

The Effect of Human Milk Oligosaccharides and Bifidobacterium longum subspecies infantis Bi-26 on Simulated Infant Gut Microbiome and Metabolites

by Krista Salli, Johanna Hirvonen, Heli Anglenius, Ashley A. Hibberd, Ilmari Ahonen, Markku T. Saarinen, Johanna Maukonen and Arthur C. Ouwehand

Microorganisms 2023, 11(6), 1553; https://doi.org/10.3390/microorganisms11061553 - 10 Jun 2023

Cited by 3 | Viewed by 1958

Abstract

Human milk oligosaccharides (HMOs) shape the developing infant gut microbiota. In this study, a semi-continuous colon simulator was used to evaluate the effect of 2 HMOs—2′-fucosyllactose (2′-FL) and 3-fucosyllactose (3-FL)—on the composition of infant faecal microbiota and microbial metabolites. The simulations were performed [...] Read more.

Human milk oligosaccharides (HMOs) shape the developing infant gut microbiota. In this study, a semi-continuous colon simulator was used to evaluate the effect of 2 HMOs—2′-fucosyllactose (2′-FL) and 3-fucosyllactose (3-FL)—on the composition of infant faecal microbiota and microbial metabolites. The simulations were performed with and without a probiotic Bifidobacterium longum subspecies infantis Bi-26 (Bi-26) and compared with a control that lacked an additional carbon source. The treatments with HMOs decreased α-diversity and increased Bifidobacterium species versus the control, but the Bifidobacterium species differed between simulations. The levels of acetic acid and the sum of all short-chain fatty acids (SCFAs) trended toward an increase with 2′-FL, as did lactic acid with 2′-FL and 3-FL, compared with control. A clear correlation was seen between the consumption of HMOs and the increase in SCFAs (−0.72) and SCFAs + lactic acid (−0.77), whereas the correlation between HMO consumption and higher total bifidobacterial numbers was moderate (−0.46). Bi-26 decreased propionic acid levels with 2′-FL. In conclusion, whereas infant faecal microbiota varied between infant donors, the addition of 2′-FL and 3-FL, alone or in combination, increased the relative abundance and numbers Bifidobacterium species in the semi-continuous colon simulation model, correlating with the production of microbial metabolites. These findings may suggest that HMOs and probiotics benefit the developing infant gut microbiota. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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10 pages, 1737 KiB

Open AccessArticle

MPrESS: An R-Package for Accurately Predicting Power for Comparisons of 16S rRNA Microbiome Taxa Distributions including Simulation by Dirichlet Mixture Modeling

by Thomas H. Clarke, Chris Greco, Lauren Brinkac, Karen E. Nelson and Harinder Singh

Microorganisms 2023, 11(5), 1166; https://doi.org/10.3390/microorganisms11051166 - 29 Apr 2023

Viewed by 1366

Abstract

Deep sequencing has revealed that the 16S rRNA gene composition of the human microbiome can vary between populations. However, when existing data are insufficient to address the desired study questions due to limited sample sizes, Dirichlet mixture modeling (DMM) can simulate 16S rRNA [...] Read more.

Deep sequencing has revealed that the 16S rRNA gene composition of the human microbiome can vary between populations. However, when existing data are insufficient to address the desired study questions due to limited sample sizes, Dirichlet mixture modeling (DMM) can simulate 16S rRNA gene predictions from experimental microbiome data. We examined the extent to which simulated 16S rRNA gene microbiome data can accurately reflect the diversity within that identified from experimental data and calculate the power. Even when experimental and simulated datasets differed by less than 10%, simulation by DMM consistently overestimates power, except when using only highly discriminating taxa. Admixtures of DMM with experimental data performed poorly compared to pure simulation and did not show the same correlation with experimental data p-value and power values. While multiple replications of random sampling remain the favored method of determining the power, when the estimated sample size required to achieve a certain power exceeds the sample number, then simulated samples based on DMM can be used. We introduce an R-Package, MPrESS, to assist in power calculation and sample size estimation for a 16S rRNA gene microbiome dataset to detect a difference between populations. MPrESS can be downloaded from GitHub. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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Review

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24 pages, 429 KiB

Open AccessReview

Animal and In Vitro Models as Powerful Tools to Decipher the Effects of Enteric Pathogens on the Human Gut Microbiota

by Marco Calvigioni, Diletta Mazzantini, Francesco Celandroni and Emilia Ghelardi

Microorganisms 2024, 12(1), 67; https://doi.org/10.3390/microorganisms12010067 - 29 Dec 2023

Cited by 1 | Viewed by 2620

Abstract

Examining the interplay between intestinal pathogens and the gut microbiota is crucial to fully comprehend the pathogenic role of enteropathogens and their broader impact on human health. Valid alternatives to human studies have been introduced in laboratory practice to evaluate the effects of [...] Read more.

Examining the interplay between intestinal pathogens and the gut microbiota is crucial to fully comprehend the pathogenic role of enteropathogens and their broader impact on human health. Valid alternatives to human studies have been introduced in laboratory practice to evaluate the effects of infectious agents on the gut microbiota, thereby exploring their translational implications in intestinal functionality and overall health. Different animal species are currently used as valuable models for intestinal infections. In addition, considering the recent advances in bioengineering, futuristic in vitro models resembling the intestinal environment are also available for this purpose. In this review, the impact of the main human enteropathogens (i.e., Clostridioides difficile, Campylobacter jejuni, diarrheagenic Escherichia coli, non-typhoidal Salmonella enterica, Shigella flexneri and Shigella sonnei, Vibrio cholerae, and Bacillus cereus) on intestinal microbial communities is summarized, with specific emphasis on results derived from investigations employing animal and in vitro models. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

16 pages, 2366 KiB

Open AccessReview

Microfluidics: Insights into Intestinal Microorganisms

by Ping Qi, Jin Lv, Xiangdong Yan, Liuhui Bai and Lei Zhang

Microorganisms 2023, 11(5), 1134; https://doi.org/10.3390/microorganisms11051134 - 27 Apr 2023

Cited by 1 | Viewed by 1938

Abstract

Microfluidics is a system involving the treatment or manipulation of microscale (10⁻⁹ to 10⁻¹⁸ L) fluids using microchannels (10 to 100 μm) contained on a microfluidic chip. Among the different methodologies used to study intestinal microorganisms, new methods based on microfluidic [...] Read more.

Microfluidics is a system involving the treatment or manipulation of microscale (10⁻⁹ to 10⁻¹⁸ L) fluids using microchannels (10 to 100 μm) contained on a microfluidic chip. Among the different methodologies used to study intestinal microorganisms, new methods based on microfluidic technology have been receiving increasing attention in recent years. The intestinal tracts of animals are populated by a vast array of microorganisms that have been established to play diverse functional roles beneficial to host physiology. This review is the first comprehensive coverage of the application of microfluidics technology in intestinal microbial research. In this review, we present a brief history of microfluidics technology and describe its applications in gut microbiome research, with a specific emphasis on the microfluidic technology-based intestine-on-a-chip, and also discuss the advantages and application prospects of microfluidic drug delivery systems in intestinal microbial research. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota)

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