Effects of Probiotic Bacteria Lactobacillaceae on the Gut Microbiota in Children With Celiac Disease Autoimmunity: A Placebo-Controlled and Randomized Clinical Trial

Disturbances of the gut microbiota may influence the development of various autoimmune diseases. This study investigated the effects of supplementations with the probiotic bacteria, Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2, on the microbial community in children with celiac disease autoimmunity (CDA). The study included 78 genetically predisposed children for celiac disease with elevated levels of tissue transglutaminase autoantibodies (tTGA) signaling for ongoing CDA. Among those children, 38 received a placebo and 40 received the probiotic supplement daily for 6 months. Fecal and plasma samples were collected at baseline and after 3 and 6 months, respectively. The bacterial community was investigated with 16S rRNA gene sequencing and terminal restriction fragment length polymorphism (T-RFLP), and tTGA levels were measured in radiobinding assays. In children that received probiotic supplementation, the relative abundance of Lactobacillaceae increased over time, while it remained unchanged in the placebo group. There was no overall correlation between tTGA levels and bacterial genus except for a positive correlation between Dialister and IgG-tTG in the probiotic group. The abundance of specific bacterial amplicon sequence variant (ASV:s) changed during the study in both groups, indicating that specific bacterial strains might be affected by probiotic supplementation.

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Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls

10.1101/227272 ◽

2017 ◽

Author(s):

Rahul Bodkhe ◽

Sudarshan A. Shetty ◽

Dhiraj P. Dhotre ◽

Anil K. Verma ◽

Khushbo Bhatia ◽

...

Keyword(s):

Celiac Disease ◽

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Sequence Variant ◽

First Degree Relatives ◽

Adult Celiac Disease ◽

Disease Site ◽

Rrna Gene Sequencing ◽

And Control

AbstractRecent studies on celiac disease (CeD) have shown the role of gut microbiota alterations in CeD pathogenesis. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific taxa between pre-diseases and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to faecal samples indicating larger disruption of microbiota at disease site. Increased abundance of specific Helicobacter ASVs were observed in duodenum of CeD when compared to FDR (p < 0.01). In case of fecal samples CeD microbiome and Actinomyces. In addition, predicted functional metagenome showed reduced ability of gluten that ecosystem level diversity measures (except in the duodenum) were not significantly different is characterized by reduced abundance of beneficial taxa such as Akkermansia, Ruminococcus degradation by CeD faecal microbiota in comparison to FDRs and controls.

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Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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Gut microbiota markers associated with obesity and overweight in Italian adults

Scientific Reports ◽

10.1038/s41598-021-84928-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Vanessa Palmas ◽

Silvia Pisanu ◽

Veronica Madau ◽

Emanuela Casula ◽

Andrea Deledda ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Smoking Status ◽

16S Rrna Gene Sequencing ◽

Normal Weight ◽

Activity Level ◽

Rrna Gene ◽

Illumina Platform ◽

Obesity And Overweight ◽

Rrna Gene Sequencing

AbstractIn the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.

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Gut microbiota accelerates cisplatin-induced acute liver injury associated with robust inflammation and oxidative stress in mice

Journal of Translational Medicine ◽

10.1186/s12967-021-02814-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Shenhai Gong ◽

Yinglin Feng ◽

Yunong Zeng ◽

Huanrui Zhang ◽

Meiping Pan ◽

...

Keyword(s):

Oxidative Stress ◽

16S Rrna ◽

Gut Microbiota ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Metabolomic Analysis ◽

Rrna Gene Sequencing ◽

And Oxidative Stress

Abstract Background Gut microbiota has been reported to be disrupted by cisplatin, as well as to modulate chemotherapy toxicity. However, the precise role of intestinal microbiota in the pathogenesis of cisplatin hepatotoxicity remains unknown. Methods We compared the composition and function of gut microbiota between mice treated with and without cisplatin using 16S rRNA gene sequencing and via metabolomic analysis. For understanding the causative relationship between gut dysbiosis and cisplatin hepatotoxicity, antibiotics were administered to deplete gut microbiota and faecal microbiota transplantation (FMT) was performed before cisplatin treatment. Results 16S rRNA gene sequencing and metabolomic analysis showed that cisplatin administration caused gut microbiota dysbiosis in mice. Gut microbiota ablation by antibiotic exposure protected against the hepatotoxicity induced by cisplatin. Interestingly, mice treated with antibiotics dampened the mitogen-activated protein kinase pathway activation and promoted nuclear factor erythroid 2-related factor 2 nuclear translocation, resulting in decreased levels of both inflammation and oxidative stress in the liver. FMT also confirmed the role of microbiota in individual susceptibility to cisplatin-induced hepatotoxicity. Conclusions This study elucidated the mechanism by which gut microbiota mediates cisplatin hepatotoxicity through enhanced inflammatory response and oxidative stress. This knowledge may help develop novel therapeutic approaches that involve targeting the composition and metabolites of microbiota.

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Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

Scientific Reports ◽

10.1038/s41598-021-82726-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Francesco Durazzi ◽

Claudia Sala ◽

Gastone Castellani ◽

Gerardo Manfreda ◽

Daniel Remondini ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Shotgun Sequencing ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Experimental Conditions ◽

Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

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Infant Gut Microbiota Associated with Fine Motor Skills

Nutrients ◽

10.3390/nu13051673 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1673

Author(s):

Inmaculada Acuña ◽

Tomás Cerdó ◽

Alicia Ruiz ◽

Francisco J. Torres-Espínola ◽

Ana López-Moreno ◽

...

Keyword(s):

Gut Microbiota ◽

Infant Development ◽

16S Rrna Gene Sequencing ◽

Fine Motor ◽

Rrna Gene ◽

Neurodevelopmental Outcomes ◽

Gut Colonization ◽

Healthy Infants ◽

Behavioural Characteristics ◽

Rrna Gene Sequencing

BACKGROUND: During early life, dynamic gut colonization and brain development co-occur with potential cross-talk mechanisms affecting behaviour. METHODS: We used 16S rRNA gene sequencing to examine the associations between gut microbiota and neurodevelopmental outcomes assessed by the Bayley Scales of Infant Development III in 71 full-term healthy infants at 18 months of age. We hypothesized that children would differ in gut microbial diversity, enterotypes obtained by Dirichlet multinomial mixture analysis and specific taxa based on their behavioural characteristics. RESULTS: In children dichotomized by behavioural trait performance in above- and below-median groups, weighted Unifrac b-diversity exhibited significant differences in fine motor (FM) activity. Dirichlet multinomial mixture modelling identified two enterotypes strongly associated with FM outcomes. When controlling for maternal pre-gestational BMI and breastfeeding for up to 3 months, the examination of signature taxa in FM groups showed that Turicibacter and Parabacteroides were highly abundant in the below-median FM group, while Collinsella, Coprococcus, Enterococcus, Fusobacterium, Holdemanella, Propionibacterium, Roseburia, Veillonella, an unassigned genus within Veillonellaceae and, interestingly, probiotic Bifidobacterium and Lactobacillus were more abundant in the above-median FM group. CONCLUSIONS: Our results suggest an association between enterotypes and specific genera with FM activity and may represent an opportunity for probiotic interventions relevant to treatment for motor disorders.

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Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco

Agronomy ◽

10.3390/agronomy11071344 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1344

Author(s):

Naima Lemjiber ◽

Khalid Naamani ◽

Annabelle Merieau ◽

Abdelhi Dihazi ◽

Nawal Zhar ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Genomic Islands ◽

Rrna Gene ◽

In Planta ◽

Bacterial Strains ◽

Bacillus Altitudinis ◽

Genes Encoding ◽

Bacillus Spp ◽

Pear Trees ◽

Rrna Gene Sequencing

Bacterial burn is one of the major diseases affecting pear trees worldwide, with serious impacts on producers and economy. In Morocco, several pear trees (Pyrus communis) have shown leaf burns since 2015. To characterize the causal agent of this disease, we isolated fourteen bacterial strains from different parts of symptomatic pear trees (leaves, shoots, fruits and flowers) that were tested in planta for their pathogenicity on Louise bonne and Williams cultivars. The results showed necrotic lesions with a significant severity range from 47.63 to 57.77% on leaves of the Louise bonne cultivar inoculated with isolate B10, while the other bacterial isolates did not induce any disease symptom. 16S rRNA gene sequencing did not allow robust taxonomic discrimination of the incriminated isolate. Thus, we conducted whole-genome sequencing (WGS) and phylogenetic analyzes based on gyrA, gyrB and cdaA gene sequences, indicating that this isolate belongs to the Bacillus altitudinis species. This taxonomic classification was further confirmed by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) analyzes compared to sixty-five Bacillus spp. type strains. The genome was mined for genes encoding carbohydrate-active enzymes (CAZymes) known to play a role in the vegetal tissue degradation. 177 candidates with functions that may support the in planta phytopathogenicity results were identified. To the best of our knowledge, this is the first data reporting B. altitudinis as agent of leaf burn in P. communis in Morocco. Our dataset will improve our knowledge on spread and pathogenicity of B. altitudinis genotypes that appears as emergent phytopathogenic agent, unveiling virulence factors and their genomic location (i.e., within genomic islands or the accessory genome) to induce trees disease.

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The protective effects of yellow tea extract against loperamide-induced constipation in mice

Food & Function ◽

10.1039/d0fo02969f ◽

2021 ◽

Author(s):

Pei-Qin Cao ◽

Xiu-Ping Li ◽

Jian Ou-Yang ◽

Rong-Gang Jiang ◽

Fang-Fang Huang ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Protective Effects ◽

Rrna Gene Sequencing ◽

Tea Extract

We evaluated the effects of yellow tea extract on relieving constipation induced by loperamide and evaluated the changes of gut microbiota based on 16S rRNA gene sequencing.

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Insight Into the Potential Value of Gut Microbial Signatures for Prediction of Gestational Anemia

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.734561 ◽

2021 ◽

Vol 11 ◽

Author(s):

Hongcheng Wei ◽

Siting Deng ◽

Yufeng Qin ◽

Xu Yang ◽

Ting Chen ◽

...

Keyword(s):

Gut Microbiota ◽

Pregnant Women ◽

Predictive Value ◽

16S Rrna Gene Sequencing ◽

Well Being ◽

Rrna Gene ◽

Second Trimester ◽

Healthy Control ◽

Rrna Gene Sequencing ◽

Validation Set

The gut microbiota alternations are associated with gestational anemia (GA); however, limited predictive value for the subsequent incidence of anemia in normal gestational women has been obtained. We sought to rigorously characterise gut dysbiosis in subjects with GA and explored the potential predictive value of novel microbial signatures for the risk of developing GA. A prospective cohort of subjects with GA (n = 156) and healthy control (n = 402), all of whom were free of GA in the second trimester, by 16S rRNA gene sequencing was conducted. Microbial signatures altered dramatically in GA compared with healthy control in the second trimester. Megamonas, Veillonella, and Haemophilus were confirmed to show differential abundances in GA after adjusting for covariates. On the contrary, Lachnospiraceae and Blautia were enriched in control. Microbial co-abundance group (CAG) network was constructed. Prospectively, CAG network relatively accurately predicted upcoming GA in normal pregnant women with an AUC of 0.7738 (95%CI: 0.7171, 0.8306) and the performance was further validated in Validation set (0.8223, 95%CI: 0.7573, 0.8874). Overall, our study demonstrated that alterations in the gut microbial community were associated with anemia in pregnancy and microbial signatures could accurately predict the subsequent incidence of anemia in normal pregnant women. Our findings provided new insights into understanding the role of gut microbiota in GA, identifying high-risk individuals, and modulating gut microbiota as a therapeutic target, thus improving quality of life and well-being of women and children.

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Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.605825 ◽

2021 ◽

Vol 11 ◽

Author(s):

Shiju Xiao ◽

Guangzhong Zhang ◽

Chunyan Jiang ◽

Xin Liu ◽

Xiaoxu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Target Genes ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Phosphotransferase System ◽

Microbial Composition ◽

Kegg Pathways ◽

Significant Difference ◽

Rrna Gene Sequencing ◽

Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

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