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Microorganisms
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Host-Gut Microbiota Interactions
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Host-Gut Microbiota Interactions

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 117616

Special Issue Editor

Prof. Dr. Carl Gordon Johnston

E-Mail Website
Guest Editor
Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
Interests: human oral and gut microbiome; effects of probiotics & antibiotics; biodegradation of polycyclic aromatic hydrocarbons (PAHs); functional diversity of genes associated with pollutant degradation; water chemistry of riverine systems; tropical field ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human gut is host to a complex ecosystem of microbes from all three evolutionary domains, spanning strict anaerobic bacteria and archaea, facultative anaerobic bacteria and fungi, as well as a plethora of phages and viruses. There is much recent scientific interest in the role of the gut microbial ecosystem in host health and dysbioses (gastrointestinal (GI) diseases, obesity, cardiovascular diseases, and infection), host gut-brain axis (mental health, mental well-being, neurological development, neurological diseases, depression, and anxiety), host immune system (development, function, antibody production, white blood cell levels and activities, and microbiocidal compound production) and intestinal permeability.

Also, host-induced effects on the gut microbiome (antibiotics, prebiotics, probiotics, nutrition, processed food, host stress, and fecal transplants) are also of interest in current studies. Modern tools, such as next generation sequencing and metagenomics, have provided a glimpse into the function of this microbiome. Yet, other aspects, including molecular signaling between the host-microbiome and ecological principles (e.g. disturbance and resilience) need to be taken into account. The broad spectrum of topics requires the participation of microbiologists, molecular biologists, ecologists, immunologists, physiologists, medical doctors, andbiochemists, among many other specialists.

Prof. Dr. Carl Gordon Johnston
Guest Editor

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19 pages, 2725 KiB  
Article
Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves
by Yaoyue Wang, Qingmiao Shen, Shu Zhong, Yulin Chen and Yuxin Yang
Microorganisms 2020, 8(7), 981; https://doi.org/10.3390/microorganisms8070981 - 30 Jun 2020
Cited by 18 | Viewed by 3159
Abstract
Mulberry leaves, which have high nutritional value, have not been fully utilized. Few research systems have indicated whether mulberry leaves can replace traditional feed ingredients in goats. In this study, we investigated the effects of feeding white cashmere goats ensiled (Group E) or [...] Read more.
Mulberry leaves, which have high nutritional value, have not been fully utilized. Few research systems have indicated whether mulberry leaves can replace traditional feed ingredients in goats. In this study, we investigated the effects of feeding white cashmere goats ensiled (Group E) or sun-dried mulberry leaves (Group S) on changes in ruminal microbial communities, rumen fermentation parameters and serum biochemical indices. The control group (Group C) received a typical total mixed ration (TMR). 16S rRNA gene sequencing revealed 209 genera belonging to 19 bacterial phyla dominated by Firmicutes and Bacteroidetes. Only the relative abundances of Erysipelotrichaceae_UCG-009 were significantly different among the three groups (p < 0.05). Physiological and biochemical findings revealed that only the serum leptin concentrations were significantly decreased when mulberry leaves were added to the diets (p < 0.05). Correlation analysis revealed that Ruminococcus_2 were significantly positively correlated with the butyrate concentration. These findings suggested that supplementation with mulberry leaves only induced minor changes in the abovementioned indicators, implying that the rumen fermentation status was still stable after adding mulberry leaves to the diets. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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19 pages, 2416 KiB  
Article
Sex-Specific Associations between Gut Prevotellaceae and Host Genetics on Adiposity
by Amanda Cuevas-Sierra, José Ignacio Riezu-Boj, Elizabeth Guruceaga, Fermín Ignacio Milagro and José Alfredo Martínez
Microorganisms 2020, 8(6), 938; https://doi.org/10.3390/microorganisms8060938 - 22 Jun 2020
Cited by 28 | Viewed by 4315
Abstract
The gut microbiome has been recognized as a tool for understanding adiposity accumulation and for providing personalized nutrition advice for the management of obesity and accompanying metabolic complications. The genetic background is also involved in human energy homeostasis. In order to increase the [...] Read more.
The gut microbiome has been recognized as a tool for understanding adiposity accumulation and for providing personalized nutrition advice for the management of obesity and accompanying metabolic complications. The genetic background is also involved in human energy homeostasis. In order to increase the value of nutrigenetic dietary advice, the interplay between genetics and microbiota must be investigated. The purpose of the present study was to evaluate interactive associations between gut microbiota composition and 95 obesity-related single nucleotide polymorphisms (SNPs) searched in the literature. Oral mucosa and fecal samples from 360 normal weight, overweight and obese subjects were collected. Next generation genotyping of these 95 SNPs and fecal 16S rRNA sequencing were performed. A genetic risk score (GRS) was constructed with 10 SNPs statistically or marginally associated with body mass index (BMI). Several microbiome statistical analyses at family taxonomic level were applied (LEfSe, Canonical Correspondence Analysis, MetagenomeSeq and Random Forest), and Prevotellaceae family was found in all of them as one of the most important bacterial families associated with BMI and GRS. Thus, in this family it was further analyzed the interactive association between BMI and GRS with linear regression models. Interestingly, women with higher abundance of Prevotellaceae and higher GRS were more obese, compared to women with higher GRS and lower abundance of Prevotellaceae. These findings suggest relevant interrelationships between Prevotellaceae and the genetic background that may determine interindividual BMI differences in women, which opens the way to new precision nutrition-based treatments for obesity. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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12 pages, 2724 KiB  
Article
Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization
by Henry Reyer, Michael Oster, Ursula M. McCormack, Eduard Muráni, Gillian E. Gardiner, Siriluck Ponsuksili, Peadar G. Lawlor and Klaus Wimmers
Microorganisms 2020, 8(4), 563; https://doi.org/10.3390/microorganisms8040563 - 14 Apr 2020
Cited by 15 | Viewed by 3106
Abstract
The composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed [...] Read more.
The composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed into body weight. As a consequence, the chemical composition of digesta after duodenal and jejunal absorption processes and passage has a limited complexity affecting colonization and molecular profiles of enterocytes in the hind gut. To decipher ileal and caecal microbial ecosystems and host transcriptional profiles that are beneficial for effective use of the remaining nutrients, pigs differing in feeding efficiency were studied. Biological functions that were consistently enriched at both the gene and microbiota levels comprise immunity-related processes, which ensure the integrity of the gastrointestinal tract. In addition, the differential abundance of certain genera, including Rothia, Subdoligranulu, Leeia and Cellulosilyticum, reflects the establishment of a microbial profile that supports the digestion of endogenously indigestible dietary components in highly feed-efficient pigs. Overall, the results indicate the potential to promote these beneficial functions and further improve feed efficiency through manipulation of dietary and probiotic strategies. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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20 pages, 3713 KiB  
Article
The Exopolysaccharide of Lactobacillus fermentum UCO-979C Is Partially Involved in Its Immunomodulatory Effect and Its Ability to Improve the Resistance against Helicobacter pylori Infection
by Valeria Garcia-Castillo, Guillermo Marcial, Leonardo Albarracín, Mikado Tomokiyo, Patricia Clua, Hideki Takahashi, Haruki Kitazawa, Apolinaria Garcia-Cancino and Julio Villena
Microorganisms 2020, 8(4), 479; https://doi.org/10.3390/microorganisms8040479 - 27 Mar 2020
Cited by 17 | Viewed by 3484
Abstract
Lactobacillus fermentum UCO-979C (Lf979C) beneficially modulates the cytokine response of gastric epithelial cells and macrophages after Helicobacter pylori infection in vitro. Nevertheless, no in vivo studies were performed with this strain to confirm its beneficial immunomodulatory effects. This work evaluated whether Lf979C improves [...] Read more.
Lactobacillus fermentum UCO-979C (Lf979C) beneficially modulates the cytokine response of gastric epithelial cells and macrophages after Helicobacter pylori infection in vitro. Nevertheless, no in vivo studies were performed with this strain to confirm its beneficial immunomodulatory effects. This work evaluated whether Lf979C improves protection against H. pylori infection in mice by modulating the innate immune response. In addition, we evaluated whether its exopolysaccharide (EPS) was involved in its beneficial effects. Lf979C significantly reduced TNF-α, IL-8, and MCP-1 and augmented IFN-γ and IL-10 in the gastric mucosa of H. pylori-infected mice. The differential cytokine profile induced by Lf979C in H. pylori-infected mice correlated with an improved reduction in the pathogen gastric colonization and protection against inflammatory damage. The purified EPS of Lf979C reduced IL-8 and enhanced IL-10 levels in the gastric mucosa of infected mice, while no effect was observed for IFN-γ. This work demonstrates for the first time the in vivo ability of Lf979C to increase resistance against H. pylori infection by modulating the gastric innate immune response. In addition, we advanced knowledge of the mechanisms involved in the beneficial effects of Lf979C by demonstrating that its EPS is partially responsible for its immunomodulatory effect. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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18 pages, 1592 KiB  
Article
Differences in Gut Microbial Diversity are Driven by Drug Use and Drug Cessation by Either Compulsory Detention or Methadone Maintenance Treatment
by Qiaoyan Li, Siqi Chen, Ke Liu, Danfeng Long, Diru Liu, Zhengchao Jing and Xiaodan Huang
Microorganisms 2020, 8(3), 411; https://doi.org/10.3390/microorganisms8030411 - 13 Mar 2020
Cited by 10 | Viewed by 2918
Abstract
In this work, we investigate differences in gut microbial diversity driven by drug use or by the widely used methods for drug cessation: methadone maintenance treatment (MMT) and compulsory detention (CD). Methods: 99 participants (28 CD participants, 16 MMT patients, 27 drug users, [...] Read more.
In this work, we investigate differences in gut microbial diversity driven by drug use or by the widely used methods for drug cessation: methadone maintenance treatment (MMT) and compulsory detention (CD). Methods: 99 participants (28 CD participants, 16 MMT patients, 27 drug users, and 28 healthy controls) were selected using strict inclusion criteria. Nutritional intake and gut microbial diversity were analyzed with bioinformatics tools and SPSS 20.0. Results: Alpha diversity was not significantly different among groups, whereas beta diversity of gut microbiota and nutrient intake were significantly higher among MMT patients. Taxa were unevenly distributed between groups, with drug users having the highest proportion of Ruminococcus and MMT patients having the highest abundance of Bifidobacterium and Lactobacillus. Conclusion: Drug use, cessation method, and diet contribute to shaping human gut communities. High beta diversity among MMT patients is likely driven by methadone use and high nutrient intake, leading to increased orexin A and enrichment for beneficial bacteria, while diversity in CD participants is largely influenced by diet. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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17 pages, 2734 KiB  
Article
Effects of a Diet Supplemented with Exogenous Catalase from Penicillium notatum on Intestinal Development and Microbiota in Weaned Piglets
by Yang Li, Xilun Zhao, Lijia Zhang, Xiaoyan Zhan, Zhiguo Liu, Yong Zhuo, Yan Lin, Zhengfeng Fang, Lianqiang Che, Bin Feng, Shengyu Xu, Jian Li and De Wu
Microorganisms 2020, 8(3), 391; https://doi.org/10.3390/microorganisms8030391 - 11 Mar 2020
Cited by 14 | Viewed by 2852
Abstract
This study aims to investigate the effects of exogenous catalase (CAT), an antioxidative enzyme from microbial cultures, on intestinal development and microbiota in weaned piglets. Seventy-two weaned piglets were allotted to two groups and fed a basal diet or a basal diet containing [...] Read more.
This study aims to investigate the effects of exogenous catalase (CAT), an antioxidative enzyme from microbial cultures, on intestinal development and microbiota in weaned piglets. Seventy-two weaned piglets were allotted to two groups and fed a basal diet or a basal diet containing 2.0 g/kg exogenous CAT. Results showed that exogenous CAT increased (p < 0.05) jejunal villus height/crypt depth ratio and intestinal factors (diamine oxidase and transforming growth factor-α) concentration. Moreover, dietary CAT supplementation enhanced the antioxidative capacity, and decreased the concentration of pro-inflammatory cytokine in the jejunum mucosa. Exogenous CAT did not affect the concentration of short-chain fatty acids, but decreased the pH value in colonic digesta (p < 0.05). Interestingly, the relative abundance of Bifidobacterium and Dialister were increased (p < 0.05), while Streptococcus and Escherichia-Shigella were decreased (p < 0.05) in colonic digesta by exogenous CAT. Accordingly, decreased (p < 0.05) predicted functions related to aerobic respiration were observed in the piglets fed the CAT diet. Our study suggests a synergic response of intestinal development and microbiota to the exogenous CAT, and provides support for the application of CAT purified from microbial cultures in the feed industry. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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15 pages, 4221 KiB  
Article
Ethnic Differences Shape the Alpha but Not Beta Diversity of Gut Microbiota from School Children in the Absence of Environmental Differences
by Ke Liu, Yongling Zhang, Qinglin Li, Huan Li, Danfeng Long, Shijuan Yan, Wenjie Huang, Ruijun Long and Xiaodan Huang
Microorganisms 2020, 8(2), 254; https://doi.org/10.3390/microorganisms8020254 - 14 Feb 2020
Cited by 16 | Viewed by 4233
Abstract
Although the human gut microbiome is shaped by factors such as diet, environment, and genetic background, most studies investigating the relationship between ethnicity and microbiota have compared groups living in separate geographical locations. To isolate the effects of ethnicity on microbial diversity by [...] Read more.
Although the human gut microbiome is shaped by factors such as diet, environment, and genetic background, most studies investigating the relationship between ethnicity and microbiota have compared groups living in separate geographical locations. To isolate the effects of ethnicity on microbial diversity by minimizing environmental differences, we selected 143 school children from Han, Tibetan, and Hui populations from the same town on the Qinghai–Tibetan Plateau for fecal microbiome 16S rDNA sequencing. We characterized the diversity, identified signature taxa, and performed correlation analysis between diet and community composition. Firmicutes (47.61%) and Bacteroidetes (38.05%) were dominant phyla among the three ethnic groups; seven genera showed significant differences in relative abundance. Tibetan populations had a higher relative abundance of Oscillibacter and Barnesiella, compared with Han and Hui populations. Alpha diversity analyses (observed species, ACE, and Shannon indices) showed that the Tibetan population had the highest diversity compared to the Hui and Han groups, whereas beta diversity analysis revealed no significant differences between groups. The consumption of grains, milk, eggs, and fruits were positively correlated with specific taxa. Under similar environments and diet, ethnic background significantly contributed to differences in alpha diversity but not beta diversity of gut microbiota. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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13 pages, 1948 KiB  
Article
Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome
by Wendy S.W. Wong, Priya Sabu, Varsha Deopujari, Shira Levy, Ankit A. Shah, Nicole Clemency, Marina Provenzano, Reem Saadoon, Akhil Munagala, Robin Baker, Rajiv Baveja, Noel T. Mueller, Maria Gloria Dominguez-Bello, Kathi Huddleston, John E. Niederhuber and Suchitra K. Hourigan
Microorganisms 2020, 8(2), 179; https://doi.org/10.3390/microorganisms8020179 - 27 Jan 2020
Cited by 26 | Viewed by 3455
Abstract
The meconium microbiome may provide insight into intrauterine and peripartum exposures and the very earliest intestinal pioneering microbes. Prenatal antibiotics have been associated with later obesity in children, which is thought to be driven by microbiome dependent mechanisms. However, there is little data [...] Read more.
The meconium microbiome may provide insight into intrauterine and peripartum exposures and the very earliest intestinal pioneering microbes. Prenatal antibiotics have been associated with later obesity in children, which is thought to be driven by microbiome dependent mechanisms. However, there is little data regarding associations of prenatal or peripartum antibiotic exposure, with or without cesarean section (CS), with the features of the meconium microbiome. In this study, 16S ribosomal RNA gene sequencing was performed on bacterial DNA of meconium samples from 105 infants in a birth cohort study. After multivariable adjustment, delivery mode (p = 0.044), prenatal antibiotic use (p = 0.005) and peripartum antibiotic use (p < 0.001) were associated with beta diversity of the infant meconium microbiome. CS (vs. vaginal delivery) and peripartum antibiotics were also associated with greater alpha diversity of the meconium microbiome (Shannon and Simpson, p < 0.05). Meconium from infants born by CS (vs. vaginal delivery) had lower relative abundance of the genus Escherichia (p < 0.001). Prenatal antibiotic use and peripartum antibiotic use (both in the overall analytic sample and when restricting to vaginally delivered infants) were associated with differential abundance of several bacterial taxa in the meconium. Bacterial taxa in the meconium microbiome were also differentially associated with infant excess weight at 12 months of age, however, sample size was limited for this comparison. In conclusion, prenatal and peripartum antibiotic use along with CS delivery were associated with differences in the diversity and composition of the meconium microbiome. Whether or not these differences in the meconium microbiome portend risk for long-term health outcomes warrants further exploration. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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15 pages, 3023 KiB  
Article
ZnO Modulates Swine Gut Microbiota and Improves Growth Performance of Nursery Pigs When Combined with Peptide Cocktail
by Xiaoyuan Wei, Tsungcheng Tsai, Joshua Knapp, Kristopher Bottoms, Feilong Deng, Robert Story, Charles Maxwell and Jiangchao Zhao
Microorganisms 2020, 8(2), 146; https://doi.org/10.3390/microorganisms8020146 - 21 Jan 2020
Cited by 24 | Viewed by 3623
Abstract
Zinc has been very efficacious in reducing post-weaning diarrhea, whereas animal-derived peptides are suggested to improve the growth performance of weaned piglets. However, the combined effect of zinc and peptides on swine production and swine gut microbiota is still largely unknown. In this [...] Read more.
Zinc has been very efficacious in reducing post-weaning diarrhea, whereas animal-derived peptides are suggested to improve the growth performance of weaned piglets. However, the combined effect of zinc and peptides on swine production and swine gut microbiota is still largely unknown. In this study, we followed 288 nursery pigs from the age of d30 to d60 to evaluate the growth performance and gut microbiota of weanling pigs subjected to different levels of a fish-porcine-microbial peptide cocktail (0.05%, 0.25%, and 0.5%) with or without the pharmaceutical level of zinc oxide (ZnO) (2500 ppm) supplementation in a nutrient-deficient diet. Rectal swab samples were collected from pigs with body weight (BW) approach average at each pen on d30, d42, and d60 to determine gut microbiota. Average daily gain (ADG) and BW in piglets fed high zinc (HZ) increased with increasing levels of peptide. The microbiota of the HZ group also diverged from those of the standard zinc (SZ) group from d30 to d60. Adding peptide did not alter community structure regardless of zinc supplementation. Collectively, these findings demonstrated that the pharmaceutical level of zinc as ZnO conditioned the gut community to the point where peptide could effectively restore growth performance in nursery pigs fed nutrient-deficient diets. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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12 pages, 1832 KiB  
Article
Hafnia alvei HA4597 Strain Reduces Food Intake and Body Weight Gain and Improves Body Composition, Glucose, and Lipid Metabolism in a Mouse Model of Hyperphagic Obesity
by Nicolas Lucas, Romain Legrand, Camille Deroissart, Manon Dominique, Saïda Azhar, Marie-Anne Le Solliec, Fatima Léon, Jean-Claude do Rego, Pierre Déchelotte, Sergueï O. Fetissov and Grégory Lambert
Microorganisms 2020, 8(1), 35; https://doi.org/10.3390/microorganisms8010035 - 23 Dec 2019
Cited by 27 | Viewed by 6639
Abstract
Use of new generation probiotics may become an integral part of the prevention and treatment strategies of obesity. The aim of the present study was to test the efficacy of a potential probiotic strain of lactic bacteria Hafnia alvei (H. alvei) [...] Read more.
Use of new generation probiotics may become an integral part of the prevention and treatment strategies of obesity. The aim of the present study was to test the efficacy of a potential probiotic strain of lactic bacteria Hafnia alvei (H. alvei) HA4597™, in a mouse model of obesity characterized by both hyperphagia and diet-induced adiposity. For this purpose, 10-week-old high-fat-diet (HFD)-fed hyperphagic ob/ob male mice received a daily treatment with 1.4 × 1010 CFU of H. alvei for 38 days. Effects of H. alvei were compared to those of a lipase inhibitor orlistat (80 mg/kg daily) and a vehicle (NaCl 0.9%) in HFD-fed ob/ob mice. A control untreated group of ob/ob mice received the standard diet throughout the experiment. The vehicle-treated HFD group displayed increased food intake, worsening of adiposity, and glycemia. Treatment with H. alvei was accompanied by decreased body weight and fat-mass gain along with reduced food intake to the level of the standard-diet-fed mice. At the end of the experiment, the group treated with H. alvei showed a decrease of glycemia, plasma total cholesterol, and alanine aminotransferase. The orlistat-treated mice showed a lower rate of body weight gain but were hyperphagic and hyperglycemic. These results demonstrate the beneficial anti-obesity and metabolic effects of H. alvei HA4597™ in mice with obesity resulting from hyperphagia and diet-induced adiposity. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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15 pages, 1036 KiB  
Article
Effects of Linoleic Acid on Gut-Derived Bifidobacterium breve DSM 20213: A Transcriptomic Approach
by Alice Senizza, Maria Luisa Callegari, Biancamaria Senizza, Andrea Minuti, Gabriele Rocchetti, Lorenzo Morelli and Vania Patrone
Microorganisms 2019, 7(12), 710; https://doi.org/10.3390/microorganisms7120710 - 17 Dec 2019
Cited by 13 | Viewed by 3554
Abstract
Bacterial production of conjugated linoleic acid (CLA) has recently received great attention because of the potential health benefits of this fatty acid. Linoleic acid (LA) can be converted to CLA by several microorganisms, including bifidobacteria, possibly as a detoxification mechanism to avoid the [...] Read more.
Bacterial production of conjugated linoleic acid (CLA) has recently received great attention because of the potential health benefits of this fatty acid. Linoleic acid (LA) can be converted to CLA by several microorganisms, including bifidobacteria, possibly as a detoxification mechanism to avoid the growth inhibition effect of LA. In the present in vitro study, we investigated the gene expression landscape of the intestinal strain Bifidobacterium breve DSM 20213 when exposed to LA. Transcriptomic analysis using RNA-seq revealed that LA induced a multifactorial stress response in the test strain, including upregulation of genes involved in iron uptake and downregulation of genes involved in sugar and oligopeptide transport. We also observed reduced transcription of genes involved in membrane and pili biosynthesis. The upregulation of iron uptake was not related to any putative ability of LA to chelate Fe2+, but was somewhat linked to stress response. Furthermore, we demonstrated that LA increased reactive oxygen species (ROS) production in bacterial cells, activating an oxidative stress response. This response was proved by thioredoxin reductase transcription, and was primarily evident among bacteria cultured in the absence of cysteine. This is the first report of the potential mechanisms involved in bacterial LA transport and stress response in B. breve. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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11 pages, 555 KiB  
Article
Modulation of Gut Microbiota by Glucosamine and Chondroitin in a Randomized, Double-Blind Pilot Trial in Humans
by Sandi L. Navarro, Lisa Levy, Keith R. Curtis, Johanna W. Lampe and Meredith A.J. Hullar
Microorganisms 2019, 7(12), 610; https://doi.org/10.3390/microorganisms7120610 - 23 Nov 2019
Cited by 11 | Viewed by 3924
Abstract
Glucosamine and chondroitin (G&C), typically taken for joint pain, are among the most frequently used specialty supplements by US adults. More recently, G&C have been associated with lower incidence of colorectal cancer in human observational studies and reduced severity of experimentally-induced ulcerative colitis [...] Read more.
Glucosamine and chondroitin (G&C), typically taken for joint pain, are among the most frequently used specialty supplements by US adults. More recently, G&C have been associated with lower incidence of colorectal cancer in human observational studies and reduced severity of experimentally-induced ulcerative colitis in rodents. However, little is known about their effects on colon-related physiology. G&C are poorly absorbed and therefore metabolized by gut microbiota. G&C have been associated with changes in microbial structure, which may alter host response. We conducted a randomized, double-blind, placebo-controlled crossover trial in ten healthy adults to evaluate the effects of a common dose of G&C compared to placebo for 14 days on gut microbial community structure, measured by 16S rRNA gene sequencing. Linear mixed models were used to evaluate the effect of G&C compared to placebo on fecal microbial alpha and beta diversity, seven phyla, and 137 genera. Nine genera were significantly different between interventions (False Discovery Rate < 0.05). Abundances of four Lachnospiraceae genera, two Prevotellaceae genera, and Desulfovibrio were increased after G&C compared to placebo, while Bifidobacterium and a member of the Christensenellaceae family were decreased. Our results suggest that G&C affect the composition of the gut microbiome which may have implications for therapeutic efficacy. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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21 pages, 3362 KiB  
Article
The Signature Microbiota Drive Rumen Function Shifts in Goat Kids Introduced to Solid Diet Regimes
by Xiaokang Lv, Jianmin Chai, Qiyu Diao, Wenqin Huang, Yimin Zhuang and Naifeng Zhang
Microorganisms 2019, 7(11), 516; https://doi.org/10.3390/microorganisms7110516 - 31 Oct 2019
Cited by 43 | Viewed by 4268
Abstract
The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an [...] Read more.
The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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18 pages, 1182 KiB  
Article
The Human Milk Microbiota is Modulated by Maternal Diet
by Marina Padilha, Niels Banhos Danneskiold-Samsøe, Asker Brejnrod, Christian Hoffmann, Vanessa Pereira Cabral, Julia de Melo Iaucci, Cristiane Hermes Sales, Regina Mara Fisberg, Ramon Vitor Cortez, Susanne Brix, Carla Romano Taddei, Karsten Kristiansen and Susana Marta Isay Saad
Microorganisms 2019, 7(11), 502; https://doi.org/10.3390/microorganisms7110502 - 29 Oct 2019
Cited by 58 | Viewed by 7815
Abstract
Human milk microorganisms contribute not only to the healthy development of the immune system in infants, but also in shaping the gut microbiota. We evaluated the effect of the maternal diet during pregnancy and during the first month of lactation on the human [...] Read more.
Human milk microorganisms contribute not only to the healthy development of the immune system in infants, but also in shaping the gut microbiota. We evaluated the effect of the maternal diet during pregnancy and during the first month of lactation on the human milk microbiota in a cross-sectional study including 94 healthy lactating women. Microbiota composition was determined by 16S rDNA profiling and nutrient intake assessed through food questionnaires. Thirteen genera were present in at least 90% of all samples, with three genera present in all samples: Streptococcus, Staphylococcus, and Corynebacterium. Cluster analysis indicated two distinct compositions: one marked by a high abundance of Streptococcus (cluster 1), and other by a high abundance of Staphylococcus (cluster 2). A global association with milk microbiota diversity was observed for vitamin C intake during pregnancy (p = 0.029), which was higher for cluster 2 individuals (cluster 2 median = 232 mg/d; cluster 1 = 175 mg/d; p = 0.02). Positive correlations were found between Bifidobacterium in the milk and intake of polyunsaturated and linoleic fatty acids during the lactation period (p < 0.01). We show that maternal diet influences the human milk microbiota, especially during pregnancy, which may contribute in shaping the gut microbiota. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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12 pages, 2067 KiB  
Article
Systematic Culturomics Shows that Half of Chicken Caecal Microbiota Members can be Grown in Vitro Except for Two Lineages of Clostridiales and a Single Lineage of Bacteroidetes
by Magdalena Crhanova, Daniela Karasova, Helena Juricova, Jitka Matiasovicova, Eva Jahodarova, Tereza Kubasova, Zuzana Seidlerova, Alois Cizek and Ivan Rychlik
Microorganisms 2019, 7(11), 496; https://doi.org/10.3390/microorganisms7110496 - 28 Oct 2019
Cited by 28 | Viewed by 3580
Abstract
Epidemiological data show that the composition of gut microbiota influences host health, disease status, and even behaviour. However, to confirm these epidemiological observations in controlled experiments, pure cultures of gut anaerobes must be obtained. Since the culture of gut anaerobes is not a [...] Read more.
Epidemiological data show that the composition of gut microbiota influences host health, disease status, and even behaviour. However, to confirm these epidemiological observations in controlled experiments, pure cultures of gut anaerobes must be obtained. Since the culture of gut anaerobes is not a simple task due to the large number of bacterial species colonising the intestinal tract, in this study we inoculated 174 different culture media with caecal content from adult hens, and compared the microbiota composition in the original caecal samples and in bacterial masses growing in vitro by 16S rRNA sequencing. In total, 42% of gut microbiota members could be grown in vitro and since there were some species which were not cultured but for which the culture conditions are known, it is likely that more than half of chicken gut microbiota can be grown in vitro. However, there were two lineages of Clostridiales and a single lineage of Bacteroidetes which were common in chicken caecal microbiota but resistant to culture. Of the most selective culture conditions, nutrient broths supplemented with mono- or di-saccharides, including those present in fruits, positively selected for Lactobacillaceae. The addition of bile salts selected for Veillonellaceae and YCFA (yeast casitone fatty acid agar) enriched for Desulfovibrionaceae. In addition, Erysipelotrichaceae were positively selected by colistin, trimethoprim, streptomycin and nalidixic acid. Culture conditions tested in this study can be used for the selective enrichment of desired bacterial species but also point towards the specific functions of individual gut microbiota members. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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20 pages, 3900 KiB  
Article
Probiotics Prevents Sensitization to Oral Antigen and Subsequent Increases in Intestinal Tight Junction Permeability in Juvenile–Young Adult Rats
by Janyerkye Tulyeu, Hideki Kumagai, Eriko Jimbo, Shinya Watanabe, Koji Yokoyama, Longzhu Cui, Hitoshi Osaka, Makiko Mieno and Takanori Yamagata
Microorganisms 2019, 7(10), 463; https://doi.org/10.3390/microorganisms7100463 - 16 Oct 2019
Cited by 28 | Viewed by 4699
Abstract
Increased intestinal permeability is thought to underlie the pathogenesis of food allergy. We explore the mechanism responsible for changes in the morphology and function of the intestinal barrier using a rat model of food allergy, focusing on the contribution of intestinal microbiota. Juvenile–young [...] Read more.
Increased intestinal permeability is thought to underlie the pathogenesis of food allergy. We explore the mechanism responsible for changes in the morphology and function of the intestinal barrier using a rat model of food allergy, focusing on the contribution of intestinal microbiota. Juvenile–young adult rats were sensitized with ovalbumin and treated with antibiotics or probiotics (Clostridium butyricum and Lactobacillus reuteri), respectively. The serum ovalbumin-IgE levels, intestinal permeability, histopathological features, tight junction (TJ)-associated proteins, Th2 cytokines, and gut microbiota in feces were analyzed in each group. Sensitized rats showed an increase in ovalbumin-IgE levels and intestinal permeability with gut mucosal inflammation, whereas rats that received probiotics were only mildly affected. Rats given ovalbumin, but not those given probiotics, showed a reduction in both TJ-related protein expression and localization. Th2 cytokine levels were increased in the sensitized rats, but not in those given probiotics. TJs in rats treated with ovalbumin and antibiotics were disrupted, but those in rats administered probiotics were undamaged. Clostridiaceae were increased in the probiotics groups, especially Alkaliphilus, relative to the ovalbumin-sensitized group. Gut microbiota appears to play a role in regulating epithelial barrier function, and probiotics may help to prevent food sensitization through the up-regulation of TJ proteins. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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18 pages, 3365 KiB  
Article
Colonization of Germ-Free Piglets with Commensal Lactobacillus amylovorus, Lactobacillus mucosae, and Probiotic E. coli Nissle 1917 and Their Interference with Salmonella Typhimurium
by Igor Splichal, Sharon M. Donovan, Zdislava Splichalova, Vera Neuzil Bunesova, Eva Vlkova, Vera Jenistova, Jiri Killer, Roman Svejstil, Eva Skrivanova and Alla Splichalova
Microorganisms 2019, 7(8), 273; https://doi.org/10.3390/microorganisms7080273 - 20 Aug 2019
Cited by 12 | Viewed by 4479
Abstract
Non-typhoid Salmonellae are worldwide spread food-borne pathogens that cause diarrhea in humans and animals. Their multi-drug resistances require alternative ways to combat this enteric pathogen. Mono-colonization of a gnotobiotic piglet gastrointestinal tract with commensal lactobacilli Lactobacillus amylovorus and Lactobacillus mucosae and with probiotic [...] Read more.
Non-typhoid Salmonellae are worldwide spread food-borne pathogens that cause diarrhea in humans and animals. Their multi-drug resistances require alternative ways to combat this enteric pathogen. Mono-colonization of a gnotobiotic piglet gastrointestinal tract with commensal lactobacilli Lactobacillus amylovorus and Lactobacillus mucosae and with probiotic E. coli Nissle 1917 and their interference with S. Typhimurium infection was compared. The impact of bacteria and possible protection against infection with Salmonella were evaluated by clinical signs, bacterial translocation, intestinal histology, mRNA expression of villin, claudin-1, claudin-2, and occludin in the ileum and colon, and local intestinal and systemic levels of inflammatory cytokines IL-8, TNF-α, and IL-10. Both lactobacilli colonized the gastrointestinal tract in approximately 100× lower density compare to E. coli Nissle and S. Typhimurium. Neither L. amylovorus nor L. mucosae suppressed the inflammatory reaction caused by the 24 h infection with S. Typhimurium. In contrast, probiotic E. coli Nissle 1917 was able to suppress clinical signs, histopathological changes, the transcriptions of the proteins, and the inductions of the inflammatory cytokines. Future studies are needed to determine whether prebiotic support of the growth of lactobacilli and multistrain lactobacilli inoculum could show higher protective effects. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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17 pages, 2064 KiB  
Article
Isolation and Immunocharacterization of Lactobacillus salivarius from the Intestine of Wakame-Fed Pigs to Develop Novel “Immunosynbiotics”
by Yuki Masumizu, Binghui Zhou, A.K.M. Humayun Kober, Md. Aminul Islam, Hikaru Iida, Wakako Ikeda-Ohtsubo, Yoshihito Suda, Leonardo Albarracin, Tomonori Nochi, Hisashi Aso, Keiichi Suzuki, Julio Villena and Haruki Kitazawa
Microorganisms 2019, 7(6), 167; https://doi.org/10.3390/microorganisms7060167 - 06 Jun 2019
Cited by 16 | Viewed by 5056
Abstract
Emerging threats of antimicrobial resistance necessitate the exploration of effective alternatives for healthy livestock growth strategies. ‘Immunosynbiotics’, a combination of immunoregulatory probiotics and prebiotics with synergistic effects when used together in feed, would be one of the most promising candidates. Lactobacilli are normal [...] Read more.
Emerging threats of antimicrobial resistance necessitate the exploration of effective alternatives for healthy livestock growth strategies. ‘Immunosynbiotics’, a combination of immunoregulatory probiotics and prebiotics with synergistic effects when used together in feed, would be one of the most promising candidates. Lactobacilli are normal residents of the gastrointestinal tract of pigs, and many of them are able to exert beneficial immunoregulatory properties. On the other hand, wakame (Undaria pinnafida), an edible seaweed, has the potential to be used as an immunoregulatory prebiotic when added to livestock feed. Therefore, in order to develop a novel immunosynbiotic, we isolated and characterized immunoregulatory lactobacilli with the ability to utilize wakame. Following a month-long in vivo wakame feeding trial in 8-week-old Landrace pigs (n = 6), sections of intestinal mucous membrane were processed for bacteriological culture and followed by identification of pure colonies by 16S rRNA sequence. Each isolate was characterized in vitro in terms of their ability to assimilate to the wakame and to differentially modulate the expression of interleukin-6 (IL-6) and interferon beta (IFN-β) in the porcine intestinal epithelial (PIE) cells triggered by Toll-like receptor (TLR)-4 and TLR-3 activation, respectively. We demonstrated that feeding wakame to pigs significantly increased the lactobacilli population in the small intestine. We established a wakame-component adjusted culture media that allowed the isolation and characterization of a total of 128 Lactobacilli salivarius colonies from the gut of wakame-fed pigs. Interestingly, several L. salivarius isolates showed both high wakame assimilation ability and immunomodulatory capacities. Among the wakame assimilating isolates, L. salivarius FFIG71 showed a significantly higher capacity to upregulate the IL-6 expression, and L. salivarius FFIG131 showed significantly higher capacity to upregulate the IFN-β expression; these could be used as immunobiotic strains in combination with wakame for the development of novel immunologically active feeds for pigs. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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Review

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12 pages, 1673 KiB  
Review
Bacteriophage and the Innate Immune System: Access and Signaling
by Amanda Carroll-Portillo and Henry C. Lin
Microorganisms 2019, 7(12), 625; https://doi.org/10.3390/microorganisms7120625 - 28 Nov 2019
Cited by 41 | Viewed by 5330
Abstract
Bacteriophage and the bacteria they infect are the dominant members of the gastrointestinal microbiome. While bacteria are known to be central to maintenance of the structure, function, and health of the microbiome, it has only recently been recognized that phage too might serve [...] Read more.
Bacteriophage and the bacteria they infect are the dominant members of the gastrointestinal microbiome. While bacteria are known to be central to maintenance of the structure, function, and health of the microbiome, it has only recently been recognized that phage too might serve a critical function. Along these lines, bacteria are not the only cells that are influenced by bacteriophage, and there is growing evidence of bacteriophage effects on epithelial, endothelial, and immune cells. The innate immune system is essential to protecting the Eukaryotic host from invading microorganisms, and bacteriophage have been demonstrated to interact with innate immune cells regularly. Here, we conduct a systematic review of the varying mechanisms allowing bacteriophage to access and interact with cells of the innate immune system and propose the potential importance of these interactions. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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15 pages, 899 KiB  
Review
The Th17/Treg Cell Balance: A Gut Microbiota-Modulated Story
by Hongyu Cheng, Xiong Guan, Dekun Chen and Wentao Ma
Microorganisms 2019, 7(12), 583; https://doi.org/10.3390/microorganisms7120583 - 20 Nov 2019
Cited by 75 | Viewed by 10037
Abstract
The intestinal tract of vertebrates is normally colonized with a remarkable number of commensal microorganisms that are collectively referred to as gut microbiota. Gut microbiota has been demonstrated to interact with immune cells and to modulate specific signaling pathways involving both innate and [...] Read more.
The intestinal tract of vertebrates is normally colonized with a remarkable number of commensal microorganisms that are collectively referred to as gut microbiota. Gut microbiota has been demonstrated to interact with immune cells and to modulate specific signaling pathways involving both innate and adaptive immune processes. Accumulated evidence suggests that the imbalance of Th17 and Treg cells is associated with the development of many diseases. Herein, we emphatically present recent findings to show how specific gut microbiota organisms and metabolites shape the balance of Th17 and Treg cells. We also discuss the therapeutic potential of fecal microbiota transplantation (FMT) in diseases caused by the imbalance of Th17 and Treg cells Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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34 pages, 1939 KiB  
Review
Gut Bacteria and their Metabolites: Which One Is the Defendant for Colorectal Cancer?
by Samira Tarashi, Seyed Davar Siadat, Sara Ahmadi Badi, Mohammadreza Zali, Roberto Biassoni, Mirco Ponzoni and Arfa Moshiri
Microorganisms 2019, 7(11), 561; https://doi.org/10.3390/microorganisms7110561 - 13 Nov 2019
Cited by 24 | Viewed by 5572
Abstract
Colorectal cancer (CRC) is a worldwide health concern which requires efficient therapeutic strategies. The mechanisms underlying CRC remain an essential subject of investigations in the cancer biology field. The evaluation of human microbiota can be critical in this regard, since the disruption of [...] Read more.
Colorectal cancer (CRC) is a worldwide health concern which requires efficient therapeutic strategies. The mechanisms underlying CRC remain an essential subject of investigations in the cancer biology field. The evaluation of human microbiota can be critical in this regard, since the disruption of the normal community of gut bacteria is an important issue in the development of CRC. However, several studies have already evaluated the different aspects of the association between microbiota and CRC. The current study aimed at reviewing and summarizing most of the studies on the modifications of gut bacteria detected in stool and tissue samples of CRC cases. In addition, the importance of metabolites derived from gut bacteria, their relationship with the microbiota, and epigenetic modifications have been evaluated. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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21 pages, 4406 KiB  
Review
Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System
by Bei Yue, Xiaoping Luo, Zhilun Yu, Sridhar Mani, Zhengtao Wang and Wei Dou
Microorganisms 2019, 7(10), 440; https://doi.org/10.3390/microorganisms7100440 - 11 Oct 2019
Cited by 58 | Viewed by 11115
Abstract
Host health depends on the intestinal homeostasis between the innate/adaptive immune system and the microbiome. Numerous studies suggest that gut microbiota are constantly monitored by the host mucosal immune system, and any slight disturbance in the microbial communities may contribute to intestinal immune [...] Read more.
Host health depends on the intestinal homeostasis between the innate/adaptive immune system and the microbiome. Numerous studies suggest that gut microbiota are constantly monitored by the host mucosal immune system, and any slight disturbance in the microbial communities may contribute to intestinal immune disruption and increased susceptibility to inflammatory bowel disease (IBD), a chronic relapsing inflammatory condition of the gastrointestinal tract. Therefore, maintaining intestinal immune homeostasis between microbiota composition and the mucosal immune system is an effective approach to prevent and control IBD. The overall theme of this review is to summarize the research concerning the pathogenesis of IBD, with particular focus on the factors of gut microbiota-mucosal immune interactions in IBD. This is a comprehensive and in-depth report of the crosstalk between gut microbiota and the mucosal immune system in IBD pathogenesis, which may provide insight into the further evaluation of the therapeutic strategies for IBD. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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16 pages, 628 KiB  
Review
Role of Gut Microbiota in Hepatocarcinogenesis
by Haripriya Gupta, Gi Soo Youn, Min Jea Shin and Ki Tae Suk
Microorganisms 2019, 7(5), 121; https://doi.org/10.3390/microorganisms7050121 - 05 May 2019
Cited by 80 | Viewed by 8462
Abstract
Hepatocellular carcinoma (HCC), one of the leading causes of death worldwide, has a causal nexus with liver injury, inflammation, and regeneration that accumulates over decades. Observations from recent studies have accounted for the involvement of the gut–liver axis in the pathophysiological mechanism responsible [...] Read more.
Hepatocellular carcinoma (HCC), one of the leading causes of death worldwide, has a causal nexus with liver injury, inflammation, and regeneration that accumulates over decades. Observations from recent studies have accounted for the involvement of the gut–liver axis in the pathophysiological mechanism responsible for HCC. The human intestine nurtures a diversified colony of microorganisms residing in the host ecosystem. The intestinal barrier is critical for conserving the normal physiology of the gut microbiome. Therefore, a rupture of this barrier or dysbiosis can cause the intestinal microbiome to serve as the main source of portal-vein endotoxins, such as lipopolysaccharide, in the progression of hepatic diseases. Indeed, increased bacterial translocation is a key sign of HCC. Considering the limited number of clinical studies on HCC with respect to the microbiome, we focus on clinical as well as animal studies involving the gut microbiota, with the current understandings of the mechanism by which the intestinal dysbiosis promotes hepatocarcinogenesis. Future research might offer mechanistic insights into the specific phyla targeting the leaky gut, as well as microbial dysbiosis, and their metabolites, which represent key pathways that drive HCC-promoting microbiome-mediated liver inflammation and fibrosis, thereby restoring the gut barrier function. Full article
(This article belongs to the Special Issue Host-Gut Microbiota Interactions)
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