Microbiome study in irradiated mice treated with BIO 300, a promising radiation countermeasure

Abstract Background The mammalian gut harbors very complex and diverse microbiota that play an important role in intestinal homeostasis and host health. Exposure to radiation results in dysbiosis of the gut microbiota leading to detrimental pathophysiological changes to the host. To alleviate the effects of irradiation, several candidate countermeasures are under investigation. BIO 300, containing synthetic genistein formulated as an amorphous solid dispersion or as an aqueous suspension of nanoparticles, is a promising candidate under advanced development. The aim of this study was to investigate the effects of BIO 300 on the gut microbiome and metabolome of mice exposed to 60Co gamma-radiation. The gut microbiota and metabolome of control and drug-treated mice exposed to radiation was characterized by bacterial 16S rRNA amplicon sequencing and untargeted metabolomics. Results We found that irradiation altered the Firmicutes/Bacteroidetes ratio and significantly decreased the relative abundance of Lactobacillus, both in BIO 300-treated and control mice; however, the ratio returned to near normal levels in BIO 300-treated mice by day 14 post-irradiation. Concomitantly, we also observed corrective shifts in metabolic pathways that were perturbed after irradiation. Conclusions Overall, the data presented show that radiation exposure led to a relative depletion of commensals like Lactobacillus leading to an inflammatory metabolic phenotype while the majority of the drug-treated mice showed alleviation of this condition primarily by restoration of normal gut microbiota. These results indicate that the radioprotective effects of BIO 300, at least in part, may involve correction of the host-microbiome metabolic axis.

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Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study

Microorganisms ◽

10.3390/microorganisms9061237 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1237

Author(s):

Han-Na Kim ◽

Eun-Jeong Joo ◽

Chil-Woo Lee ◽

Kwang-Sung Ahn ◽

Hyung-Lae Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Gastrointestinal Symptoms ◽

Amplicon Sequencing ◽

Recovery Phase ◽

Fecal Samples ◽

Intestinal Microbes ◽

Gut Dysbiosis ◽

16S Rrna Amplicon Sequencing ◽

Microbiome Data ◽

Negative Conversion

Patients with COVID-19 have been reported to experience gastrointestinal symptoms as well as respiratory symptoms, but the effects of COVID-19 on the gut microbiota are poorly understood. We explored gut microbiome profiles associated with the respiratory infection of SARS-CoV-2 during the recovery phase in patients with asymptomatic or mild COVID-19. A longitudinal analysis was performed using the same patients to determine whether the gut microbiota changed after recovery from COVID-19. We applied 16S rRNA amplicon sequencing to analyze two paired fecal samples from 12 patients with asymptomatic or mild COVID-19. Fecal samples were selected at two time points: during SARS-CoV-2 infection (infected state) and after negative conversion of the viral RNA (recovered state). We also compared the microbiome data with those from 36 healthy controls. Microbial evenness of the recovered state was significantly increased compared with the infected state. SARS-CoV-2 infection induced the depletion of Bacteroidetes, while an abundance was observed with a tendency to rapidly reverse in the recovered state. The Firmicutes/Bacteroidetes ratio in the infected state was markedly higher than that in the recovered state. Gut dysbiosis was observed after infection even in patients with asymptomatic or mild COVID-19, while the composition of the gut microbiota was recovered after negative conversion of SARS-CoV-2 RNA. Modifying intestinal microbes in response to COVID-19 might be a useful therapeutic alternative.

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H. pylori Eradication Treatment Alters Gut Microbiota and GLP-1 Secretion in Humans

Journal of Clinical Medicine ◽

10.3390/jcm8040451 ◽

2019 ◽

Vol 8 (4) ◽

pp. 451 ◽

Cited By ~ 11

Author(s):

Isabel Cornejo-Pareja ◽

Gracia Martín-Núñez ◽

M. Roca-Rodríguez ◽

Fernando Cardona ◽

Leticia Coin-Aragüez ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Carbohydrate Metabolism ◽

Eradication Therapy ◽

Amplicon Sequencing ◽

Antibiotic Use ◽

Metabolic Disturbances ◽

Bifidobacterium Adolescentis ◽

16S Rrna Amplicon Sequencing ◽

H Pylori

Changes in the intestinal microbial community and some metabolic disturbances, including obesity and type2 diabetes, are related. Glucagon-like peptide-1 (GLP-1) regulates glucose homeostasis. Microbiota have been linked to incretin secretion. Antibiotic use causes changes in microbial diversity and composition. Our aim was to evaluate the relationship between microbiota changes and GLP-1 secretion. A prospective case-control study with a Helicobacter pylori-positive patient model involving subjects under eradication therapy (omeprazole, clarithromycin, and amoxicillin). Forty patients with H. pylori infection and 20 matched participants, but negative for H. pylori antigen. Patients were evaluated before and two months after treatment. We analyzed anthropometric measurements, carbohydrate metabolism, lipid profile, and C-reactive protein. Gut microbiota composition was analyzed through 16S rRNA amplicon sequencing (IlluminaMiSeq). Eradication treatment for H. pylori decreased bacterial richness (Chao1, p = 0.041). Changes in gut microbiota profiles were observed at phylum, family, genus and species levels. GLP-1 secretion and variables of carbohydrate metabolism were improved. Correlations were seen between GLP-1 changes and variations within microbial community abundances, specifically Bifidobacterium adolescentis, the Lachnobacterium genus, and Coriobacteriaceae family. A conventional treatment to eradicate H. pylori could improve carbohydrate metabolism possibly in relation with an increase in GLP-1 secretion. GLP-1 secretion may be related to alterations in intestinal microbiota, specifically Lachnobacterium, B. adolescentis and Coriobacteriaceae.

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The Effect of Lactobacillus plantarum BW2013 on The Gut Microbiota in Mice Analyzed by 16S rRNA Amplicon Sequencing

Polish Journal of Microbiology ◽

10.33073/pjm-2021-022 ◽

2021 ◽

Vol 70 (2) ◽

pp. 235-243

Author(s):

TONG TONG ◽

XIAOHUI NIU ◽

QIAN LI ◽

YUXI LING ◽

ZUMING LI ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Dose Group ◽

Low Dose ◽

Amplicon Sequencing ◽

Control Group ◽

High Dose ◽

Treatment Groups ◽

16S Rrna Amplicon Sequencing ◽

Medium Dose

Lactobacillus plantarum BW2013 was isolated from the fermented Chinese cabbage. This study aimed to test the effect of this strain on the gut microbiota in BALB/c mice by 16S rRNA amplicon sequencing. The mice were randomly allocated to the control group and three treatment groups of L. plantarum BW2013 (a low-dose group of 108 CFU/ml, a medium-dose group of 109 CFU/ml, and a high-dose group of 1010 CFU/ml). The weight of mice was recorded once a week, and the fecal samples were collected for 16S rRNA amplicon sequencing after 28 days of continuous treatment. Compared with the control group, the body weight gain in the treatment groups was not significant. The 16S rRNA amplicon sequencing analysis showed that both the Chao1 and ACE indexes increased slightly in the medium-dose group compared to the control group, but the difference was not significant. Based on PCoA results, there was no significant difference in β diversity between the treatment groups. Compared to the control group, the abundance of Bacteroidetes increased in the low-dose group. The abundance of Firmicutes increased in the medium-dose group. At the genus level, the abundance of Alloprevotella increased in the low-dose group compared to the control group. The increased abundance of Ruminococcaceae and decreased abundance of Candidatus_Saccharimonas was observed in the medium-dose group. Additionally, the abundance of Bacteroides increased, and Alistipes and Candidatus_Saccharimonas decreased in the high-dose group. These results indicated that L. plantarum BW2013 could ameliorate gut microbiota composition, but its effects vary with the dose.

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Korean Traditional Medicine (Jakyakgamcho-tang) Ameliorates Colitis by Regulating Gut Microbiota

Metabolites ◽

10.3390/metabo9100226 ◽

2019 ◽

Vol 9 (10) ◽

pp. 226 ◽

Cited By ~ 1

Author(s):

Seung-Ho Seo ◽

Tatsuya Unno ◽

Seong-Eun Park ◽

Eun-Ju Kim ◽

Yu-Mi Lee ◽

...

Keyword(s):

Gut Microbiota ◽

Amplicon Sequencing ◽

Control Group ◽

Scaling Analysis ◽

Aminosalicylic Acid ◽

Operational Taxonomic Units ◽

16S Rrna Amplicon Sequencing ◽

Cytokine Levels ◽

Korean Traditional Medicine ◽

Gut Microbial Community

The objective of this study was to examine the anti-colitis activity of Jakyakgamcho-tang (JGT) in dextran sulfate sodium (DSS)-induced colitis and explore changes of the gut microbial community using 16S rRNA amplicon sequencing and metabolomics approaches. It was found that treatment with JGT or 5-aminosalicylic acid (5-ASA) alleviated the severity of colitis symptoms by suppressing inflammatory cytokine levels of IL-6, IL-12, and IFN-γ. The non-metric multidimensional scaling analysis of gut microbiome revealed that JGT groups were clearly separated from the DSS group, suggesting that JGT administration altered gut microbiota. The operational taxonomic units (OTUs) that were decreased by DSS but increased by JGT include Akkermansia and Allobaculum. On the other hand, OTUs that were increased by DSS but decreased by 5-ASA or JGT treatments include Bacteroidales S24-7, Ruminococcaceae, and Rikenellaceae, and the genera Bacteroides, Parabacteroides, Oscillospira, and Coprobacillus. After JGT administration, the metabolites, including most amino acids and lactic acid that were altered by colitis induction, became similar to those of the control group. This study demonstrates that JGT might have potential to effectively treat colitis by restoring dysbiosis of gut microbiota and host metabolites.

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Gut Microbiota Modulation by Dietary Barley Malt Melanoidins

Nutrients ◽

10.3390/nu12010241 ◽

2020 ◽

Vol 12 (1) ◽

pp. 241 ◽

Cited By ~ 1

Author(s):

Nesreen Aljahdali ◽

Pascale Gadonna-Widehem ◽

Pauline M. Anton ◽

Franck Carbonero

Keyword(s):

Fatty Acids ◽

Gut Microbiota ◽

Amplicon Sequencing ◽

Short Chain Fatty Acids ◽

Control Group ◽

Maillard Reaction Products ◽

Reaction Products ◽

Barley Malt ◽

16S Rrna Amplicon Sequencing ◽

The Impact

Melanoidins are the final Maillard reaction products (protein–carbohydrate complexes) produced in food by prolonged and intense heating. We assessed the impact of the consumption of melanoidins from barley malts on gut microbiota. Seventy-five mice were assigned into five groups, where the control group consumed a non-melanoidin malt diet, and other groups received melanoidin-rich malts in increments of 25% up to 100% melanoidin malts. Feces were sampled at days 0, 1, 2, 3, 7, 14, and 21 and the microbiota was determined using V4 bacterial 16S rRNA amplicon sequencing and short-chain fatty acids (SCFA) by gas chromatography. Increased melanoidins was found to result in significantly divergent gut microbiota profiles and supported sustained SCFA production. The relative abundance of Dorea, Oscillibacter, and Alisitpes were decreased, while Lactobacillus, Parasutterella, Akkermansia, Bifidobacterium, and Barnesiella increased. Bifidobacterium spp. and Akkermansia spp. were significantly increased in mice consuming the highest melanoidin amounts, suggesting remarkable prebiotic potential.

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Effect of low-iron micronutrient powder (MNP) on the composition of gut microbiota of Bangladeshi children in a high-iron groundwater setting: a randomized controlled trial

European Journal of Nutrition ◽

10.1007/s00394-021-02523-1 ◽

2021 ◽

Author(s):

Sabuktagin Rahman ◽

Guus A. M. Kortman ◽

Jos Boekhorst ◽

Patricia Lee ◽

Moududur R. Khan ◽

...

Keyword(s):

Randomized Controlled Trial ◽

Gut Microbiota ◽

Treatment Effect ◽

Controlled Trial ◽

Amplicon Sequencing ◽

High Concentration ◽

Significant Treatment ◽

Randomized Controlled ◽

16S Rrna Amplicon Sequencing ◽

Micronutrient Powder

Abstract Purpose Adverse effects of iron fortification/supplements such as Micronutrient Powder (MNP) on gut microbiota have previously been found in infection-prone African settings. This study examined the adversaries of a low-iron MNP compared with the standard MNP on the composition of gut microbiota in Bangladeshi children exposed to a high concentration of iron from potable groundwater. Methods A randomized controlled trial was conducted in 2- to 5-year-old children, drinking groundwater with a high concentration of iron (≥ 2 mg/L). Children were randomized to receive one sachet per day of either standard MNP (12.5 mg iron) or low-iron MNP (5 mg iron), for 2 months. A sub-sample of 53 children was considered for paired assessment of the gut microbiome by 16S rRNA amplicon sequencing. Results At baseline, the gut microbiota consisted of Bifidobacteriaceae (15.6%), Prevotellaceae (12.2%), Lactobacillaceae (3.6%), Clostridiaceae (4.1%) and Enterobacteriaceae (2.8%). Overall, there was no significant treatment effect of the low-iron MNP compared to the standard MNP. However, an apparent treatment effect was observed in children with a relative adult-like microbiota, with a higher relative abundance of potentially pathogenic Enterobacteriaceae after receiving the standard MNP compared to the low-iron MNP. This effect, however, was statistically non-significant (p = 0.07). Conclusion In Bangladeshi children drinking iron-rich groundwater, a low-iron MNP supplementation did not have a significant impact on their gut microbiota profile/composition compared to the standard MNP. The trial registration number is ISRCTN60058115; Date of registration 03/07/2019; retrospectively registered.

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On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples

10.1101/2021.02.04.429844 ◽

2021 ◽

Author(s):

Shan Sun ◽

Xiangzhu Zhu ◽

Xiang Huang ◽

Harvey J. Murff ◽

Reid M. Ness ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Mucosal Tissue ◽

Tissue Samples ◽

16S Rrna Amplicon Sequencing ◽

Functional Profiles

AbstractThe gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizers Bacteroides and Subdoligranulum, as well as bacteria with higher tolerance for oxidative stress such as Escherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.

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Gut microbiota differences between psoriatic arthritis and undifferentiated arthritis patients

10.21203/rs.3.rs-15400/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Chung-Yuan Hsu ◽

Ho-Chang Kuo ◽

YU-JIH Su

Keyword(s):

Psoriatic Arthritis ◽

Gut Microbiota ◽

Clinical Laboratory ◽

Clinical Symptoms ◽

Biochemical Study ◽

Laboratory Data ◽

Amplicon Sequencing ◽

Joint Disease ◽

Undifferentiated Arthritis ◽

16S Rrna Amplicon Sequencing

Abstract Introduction Psoriatic arthritis (PSA) is a form of immune-mediated inflammatory arthritis. Studying the gut microbiota of PSA patients may offer new insights into the pathophysiology of this inflammatory joint disease. We designed a prospective study to examine gut microbiome from patients with PSA, primarily with enthesitis and dactylitis, and compared the data with undifferentiated arthritis patients (NO PSA), without enthesitis or dactylitis.Methods We enrolled nine PSA patients and 10 NO PSA patients in this study. The fecal samples were investigated by using 16S rRNA amplicon sequencing, followed by bioinformatics and statistical analyses. Results None of the available objective clinical laboratory data could differentiate PSA from the NO PSA subgroup. The microbiota result shows that Family: XIII_AD3011 is significantly higher in NO PSA patients than PSA patients’ stool samples (p=0.039). Megasphaera elsdenii in the PSA was 10000 times higher than in the NO PSA group.Conclusion Our results demonstrated high intra-group homogeneous and high inter-group heterogeneous microbiota. The clinical symptoms of either enthesitis or dactylitis link to the specific microbiota in the current study. In the future, a larger cohort and thorough biochemical study is needed for confirmation.

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Characterization of Gut Microbiota Associated with Clinical Parameters in Intrahepatic Cholestasis of Pregnant Patients

10.21203/rs.2.18873/v1 ◽

2019 ◽

Author(s):

Rong Li ◽

xuehai chen ◽

Zhongzhen Liu ◽

Yan Chen ◽

Chuan Liu ◽

...

Keyword(s):

Gut Microbiota ◽

Pregnant Women ◽

Intrahepatic Cholestasis ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Clinical Parameters ◽

Sequencing Data ◽

Unifrac Distance ◽

Biochemical Indices ◽

And Control

Abstract BackgroundIntrahepatic cholestasis of pregnancy (ICP) is a liver disease that specifically occurs during pregnancy. Pregnant women with ICP biochemically reflect elevated liver functions and increases in serum bilirubin levels, while clinically individuals can display symptoms of itching and have elevated risks of preterm delivery and stillbirths. We hypothesized that there linkages between gut microbiota and ICP progression exist and could be scientifically characterized. MethodsIn total, 27 patients with ICP and 31 unafflicted control patients were recruited in this study. We performed 16S rRNA gene amplicon sequencing on gut microbiota from individual fecal samples. Sequencing data was analyzed and the correlations between components of microbiota and patient ICP status were tested. Relative abundances, related metabolic pathways, and significantly different OTUs between ICP and control patients were identified.ResultsBiochemical indices including measures for bile, ALT, AST, Dbil, and Tbil, and these were found to at higher levels in ICP versus control patients. Gut microbiota in pregnant women was dominated by four major phyla and 27 core genera. PCoA analysis results indicated that there was marginal significant clustering in unweighted Unifrac distance matrices. A moderate correlation coefficient was observed between specific OTUs and measured clinical parameters of patients. When comparing relatively rare microbiota taxa, the abundance of Butyricimonas was lower, while Citrobacter, Pseudomonas, Streptococcus, and Weissella were higher in ICP patients than in control patients. No significant differences in the pathways between ICP and control patients were identified.ConclusionsOur research indicated that patients with ICP have altered phylogenetic gut microbiota profiles compared to control patients without ICP, and that the composition was associated with measurements of patient clinical parameters. These alterations may be correlated with variations of the levels of patient enteric bile acids, and may play a role in the progression of ICP.

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Alteration of Gut Microbiota After Antibiotic Exposure in Finishing Swine

Frontiers in Microbiology ◽

10.3389/fmicb.2021.596002 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hee Eun Jo ◽

Min-Sung Kwon ◽

Tae Woong Whon ◽

Doo Wan Kim ◽

Misun Yun ◽

...

Keyword(s):

Gut Microbiota ◽

Metabolic Pathways ◽

Amplicon Sequencing ◽

Swine Industry ◽

Commensal Microbiota ◽

16S Rrna Amplicon Sequencing ◽

Fiber Degradation ◽

As Species ◽

Diarrhea Incidence ◽

Gut Microbial Community

Subclinical doses of antimicrobials are commonly used in the swine industry to control infectious diseases and growth performance. Accumulating evidence suggests that swine administered with antibiotics are susceptible to disease development due to disruption of the beneficial gut microbial community, which is associated with host immune regulation, nutrient digestion, and colonization resistance against pathogens. In this study, we found that finishing swine administered with lincomycin showed gut dysbiosis and increased diarrhea incidence compared with control swine. 16S rRNA amplicon sequencing was used to analyze the gut microbiota in finishing swine administered with lincomycin. The relative abundance of detrimental microbes, such as species of Clostridium, Aerococcus, Escherichia-Shigella, and Corynebacterium was increased in the feces of lincomycin-administered finishing swine, but that of bacteria associated with fiber degradation, such as species of Treponema, Succinivibrio, Fibrobacter, and Cellulosilyticum was decreased. Moreover, administration of lincomycin significantly increased the enrichment of metabolic pathways related to pathogenicity and deficiency of polysaccharide degradation. These results suggest that lincomycin treatment could cause severe disruption of the commensal microbiota in finishing swine.

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