scholarly journals Up to Four Biannual Administrations of Mass Azithromycin Treatment Are Associated with Modest Changes in the Gut Microbiota of Rural Malawian Children

2020 ◽  
Author(s):  
David Chaima ◽  
Harry Pickering ◽  
John. D Hart ◽  
Sarah. E Burr ◽  
Joanna Houghton ◽  
...  
Keyword(s):  
Cohort Study ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Alpha Diversity ◽  
Mass Treatment ◽  
Mortality Benefit ◽  
Gut Flora ◽  
Middle Income ◽  
Fecal Samples ◽  
Rrna Sequencing

Community-level mass treatment with azithromycin has been associated with a mortality benefit in children. However, antibiotic exposures result in disruption of the gut microbiota and repeated exposures may reduce recovery of the gut flora. We conducted a nested cohort study to examine associations between mass drug administration (MDA) with azithromycin and the gut microbiota of rural Malawian children aged between 1-59 months. Fecal samples were collected from the children prior to treatment and 6 months after two or four biannual rounds of azithromycin treatment. DNA was extracted from fecal samples and V4-16S rRNA sequencing used to characterize the gut microbiota. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were the dominant phyla while Faecalibacterium and Bifidobacterium were the most prevalent genera. There were no associations between azithromycin treatment and changes in alpha diversity, however, four biannual rounds of treatment were associated with increased abundance of Prevotella. The lack of significant changes in gut microbiota after four biannual treatments supports the use of mass azithromycin treatment to reduce mortality in children living in low- and middle-income settings.

scholarly journals Effect of Antibiotics on the Gut Microbiota in Children With Chronic Pancreatitis

2021 ◽  
Author(s):  
Wei Wang ◽  
Yuan Xiao ◽  
Shuang Ma ◽  
Xinqiong Wang ◽  
Yiran Zhou ◽  
...  
Keyword(s):  
Chronic Pancreatitis ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Area Under The Curve ◽  
Alpha Diversity ◽  
Healthy Controls ◽  
Gram Positive Bacteria ◽  
Kegg Analysis ◽  
Sequencing Method ◽  
Rrna Sequencing

Abstract OBJECTIVES: Little is known about the effect of antibiotic treatment on the gut microbiota in children with chronic pancreatitis (CCP). Our objective was to identify the main gut microbiota genera and characterize these patients’ functional mutations after using antibiotics.METHODS: The 16S rRNA sequencing method was used to compare the gut microbiota of healthy controls (HCs) with CCP using and not using antibiotics.RESULTS: All CCP demonstrated a significantly reduced alpha diversity of the gut microbiota (P＜0.01). The gut microbiota's alpha diversity and the abundance of genera’s beta diversity did not show statistical differences between the non-antibiotics and antibiotics groups. There were 15 altered genera with common abundance in the non-antibiotics and antibiotics groups compared to the HC group. The area under the curve (AUC) of the top three probiotics, i.e., Faecalibacterium, Eubacterium, and Subdoligranulum, was 0.91. Among the 13 genera altered in the non-antibiotics group, the top three genera were not appropriate as biomarkers for cases receiving antibiotics. Compared to these 13 genera, the differences between the genera and the proportion of gram-positive bacteria in the 17 genera altered only in the antibiotics group were not statistically significant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the antibiotics caused alterations in the abundance of certain genera. The enriched functions and the altered gut microbiota in the two groups had their enriched functions.CONCLUSIONS: The use of antibiotics affects the gut microbiota of CCP, but the effect of disease on gut microbiota is still obvious.

scholarly journals Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

scholarly journals Antibiotic-Induced Dysbiosis of Microbiota Promotes Chicken Lipogenesis by Altering Metabolomics in the Cecum

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 487
Author(s):  
Tao Zhang ◽  
Hao Ding ◽  
Lan Chen ◽  
Yueyue Lin ◽  
Yongshuang Gong ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
High Performance ◽  
Fat Deposition ◽  
16S Rrna Sequencing ◽  
Oral Antibiotics ◽  
Ms Analysis ◽  
Rrna Sequencing ◽  
Cecal Microbiota ◽  
Metabolite Network

Elucidation of the mechanism of lipogenesis and fat deposition is essential for controlling excessive fat deposition in chicken. Studies have shown that gut microbiota plays an important role in regulating host lipogenesis and lipid metabolism. However, the function of gut microbiota in the lipogenesis of chicken and their relevant mechanisms are poorly understood. In the present study, the gut microbiota of chicken was depleted by oral antibiotics. Changes in cecal microbiota and metabolomics were detected by 16S rRNA sequencing and ultra-high performance liquid chromatography coupled with MS/MS (UHPLC–MS/MS) analysis. The correlation between antibiotic-induced dysbiosis of gut microbiota and metabolites and lipogenesis were analysed. We found that oral antibiotics significantly promoted the lipogenesis of chicken. 16S rRNA sequencing indicated that oral antibiotics significantly reduced the diversity and richness and caused dysbiosis of gut microbiota. Specifically, the abundance of Proteobacteria was increased considerably while the abundances of Bacteroidetes and Firmicutes were significantly decreased. At the genus level, the abundances of genera Escherichia-Shigella and Klebsiella were significantly increased while the abundances of 12 genera were significantly decreased, including Bacteroides. UHPLC-MS/MS analysis showed that antibiotic-induced dysbiosis of gut microbiota significantly altered cecal metabolomics and caused declines in abundance of 799 metabolites and increases in abundance of 945 metabolites. Microbiota-metabolite network revealed significant correlations between 4 differential phyla and 244 differential metabolites as well as 15 differential genera and 304 differential metabolites. Three metabolites of l-glutamic acid, pantothenate acid and N-acetyl-l-aspartic acid were identified as potential metabolites that link gut microbiota and lipogenesis in chicken. In conclusion, our results showed that antibiotic-induced dysbiosis of gut microbiota promotes lipogenesis of chicken by altering relevant metabolomics. The efforts in this study laid a basis for further study of the mechanisms that gut microbiota regulates lipogenesis and fat deposition of chicken.

scholarly journals Alterations in intestinal microbiota diversity, composition, and function in patients with sarcopenia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lin Kang ◽  
Pengtao Li ◽  
Danyang Wang ◽  
Taihao Wang ◽  
Dong Hao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
16S Rrna ◽  
Intestinal Microbiota ◽  
Muscle Growth ◽  
Growth Function ◽  
16S Rrna Sequencing ◽  
Fecal Samples ◽  
Lipopolysaccharide Biosynthesis ◽  
Rrna Sequencing ◽  
And Function

Abstract16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium—known butyrate producers—were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.

scholarly journals Effects of Transanal Irrigation on Gut Microbiota in Pediatric Patients with Spina Bifida

2021 ◽  
Vol 10 (2) ◽  
pp. 224
Author(s):  
Akira Furuta ◽  
Yasuyuki Suzuki ◽  
Ryosuke Takahashi ◽  
Birte Petersen Jakobsen ◽  
Takahiro Kimura ◽  
...  
Keyword(s):  
Spina Bifida ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Pediatric Patients ◽  
Host Immune System ◽  
Healthy Controls ◽  
Transanal Irrigation ◽  
Rrna Sequencing ◽  
Before And After ◽  
Neurogenic Bowel

Recent studies using 16S rRNA-based microbiota profiling have demonstrated dysbiosis of gut microbiota in constipated patients. The aim of this study was to investigate the changes in gut microbiota after transanal irrigation (TAI) in patients with spina bifida (SB). A questionnaire on neurogenic bowel disfunction (NBD), Bristol scale, and gut microbiota using 16S rRNA sequencing were completed in 16 SB patients and 10 healthy controls aged 6–17 years. Then, 11 of 16 SB patients with moderate to severe NBD scores received TAI for 3 months. Changes in urine cultures were also examined before and after the TAI treatments. In addition, correlation of gut microbiota and Bristol scale was analyzed. Significantly decreased abundance in Faecalibacterium, Blautia and Roseburia, and significantly increased abundance in Bacteroides and Roseburia were observed in the SB patients compared with controls and after TAI, respectively. The abundance of Roseburia was significantly correlated positively with Bristol scale. Urinary tract infection tended to decrease from 82% to 55% after TAI (p = 0.082) despite persistent fecal incontinence. Butyrate-producing bacteria such as Roseburia play a regulatory role in the intestinal motility and host immune system, suggesting the effects of TAI on gut microbiota.

scholarly journals Probiotic Supplementation in a Clostridium difficile-Infected Gastrointestinal Model Is Associated with Restoring Metabolic Function of Microbiota

2019 ◽  
Vol 8 (1) ◽  
pp. 60
Author(s):  
Mohd Baasir Gaisawat ◽  
Chad W. MacPherson ◽  
Julien Tremblay ◽  
Amanda Piano ◽  
Michèle M. Iskandar ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Alpha Diversity ◽  
Gastrointestinal Disorder ◽  
Short Chain Fatty Acids ◽  
Rrna Gene ◽  
Metabolic Function ◽  
Microbial Composition ◽  
Single Strain ◽  
Fecal Samples ◽  
Metabolic Functions

Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an adjunct is being studied extensively due to their potential to modulate metabolic functions and the gut microbiota. In the present study, we assessed the ability of several single strain probiotics and a probiotic mixture to change the metabolic functions of normal and C. difficile-infected fecal samples. The production of short-chain fatty acids (SCFAs), hydrogen sulfide (H2S), and ammonia was measured, and changes in microbial composition were assessed by 16S rRNA gene amplicon sequencing. The C. difficile-infection in fecal samples resulted in a significant decrease (p < 0.05) in SCFA and H2S production, with a lower microbial alpha diversity. All probiotic treatments were associated with significantly increased (p < 0.05) levels of SCFAs and restored H2S levels. Probiotics showed no effect on microbial composition of either normal or C. difficile-infected fecal samples. These findings indicate that probiotics may be useful to improve the metabolic dysregulation associated with C. difficile infection.

scholarly journals Comparative analysis of gut microbiota among the male, female and pregnant giant pandas (Ailuropoda Melanoleuca)

2019 ◽  
Vol 14 (1) ◽  
pp. 288-298
Author(s):  
Siyue Zhao ◽  
Caiwu Li ◽  
Guo Li ◽  
Shengzhi Yang ◽  
Yingming Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Vital Role ◽  
Ailuropoda Melanoleuca ◽  
Its Sequencing ◽  
Giant Pandas ◽  
Host Health ◽  
Rrna Sequencing

AbstractThe giant panda (GP) was the most endangered species in China, and gut microbiota plays a vital role in host health. To determine the differences of the gut microbiota among the male, female and pregnant GPs, a comparative analysis of gut microbiota in GPs was carried out by 16S rRNA and ITS high-throughput sequencing. In 16S rRNA sequencing, 435 OTUs, 17 phyla and 182 genera were totally detected. Firmicutes (53.6%) was the predominant phylum followed by Proteobacteria (37.8%) and Fusobacteria (7.1%). Escherichia/Shigella (35.9%) was the most prevalent genus followed by Streptococcus (25.9%) and Clostridium (11.1%). In ITS sequencing, 920 OTUs, 6 phyla and 322 genera were also detected. Ascomycota (71.3%) was the predominant phylum followed by Basidiomycota (28.4%) and Zygomycota (0.15%). Purpureocillium (4.4%) was the most prevalent genus followed by Cladosporium (2.5%) and Pezicula (2.4%). Comparative analysis indicated that the male GPs harbor a higher abundance of phylum Firmicutes than female GPs with the contribution from genus Streptococcus. Meanwhile, the female GPs harbor a higher abundance of phylum Proteobacteria than male GPs with the contribution from genus Escherichia/ Shigella. In addition, the shift in bacteria from female to pregnant GPs indicated that phylum Firmicutes increased significantly with the contribution from Clostridium in the gut, which may provide an opportunity to study possible associations with low reproduction of the GPs.

scholarly journals Ketonuria Is Associated with Changes to the Abundance of Roseburia in the Gut Microbiota of Overweight and Obese Women at 16 Weeks Gestation: A Cross-Sectional Observational Study

Nutrients ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1836 ◽  
Author(s):  
Helen Robinson ◽  
Helen Barrett ◽  
Luisa Gomez-Arango ◽  
H. David McIntyre ◽  
Leonie Callaway ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Pregnant Women ◽  
Clustering Analysis ◽  
Alpha Diversity ◽  
Microbiota Composition ◽  
Obese Women ◽  
Cross Sectional ◽  
Low Carbohydrate ◽  
Rrna Sequencing ◽  
Gut Microbiota Composition

The gut microbiome in pregnancy has been associated with various maternal metabolic and hormonal markers involved in glucose metabolism. Maternal ketones are of particular interest due to the rise in popularity of low-carbohydrate diets. We assessed for differences in the composition of the gut microbiota in pregnant women with and without ketonuria at 16 weeks gestation. Fecal samples were obtained from 11 women with fasting ketonuria and 11 matched controls. The samples were analyzed to assess for differences in gut microbiota composition by 16S rRNA sequencing. Supervised hierarchical clustering analysis showed significantly different beta-diversity between women with and without ketonuria, but no difference in the alpha-diversity. Group comparisons and network analysis showed that ketonuria was associated with an increased abundance of the butyrate-producing genus Roseburia. The bacteria that contributed the most to the differences in the composition of the gut microbiota included Roseburia, Methanobrevibacter, Uncl. RF39, and Dialister in women with ketonuria and Eggerthella, Phascolarctobacterium, Butyricimonas, and Uncl. Coriobacteriaceae in women without ketonuria. This study found that the genus Roseburia is more abundant in the gut microbiota of pregnant women with ketonuria. Roseburia is a butyrate producing bacterium and may increase serum ketone levels.

scholarly journals Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Marta Reyman ◽  
Marlies A. van Houten ◽  
Kayleigh Arp ◽  
Elisabeth A. M. Sanders ◽  
Debby Bogaert
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Community Composition ◽  
Clinical Settings ◽  
Strongly Correlated ◽  
Paired Samples ◽  
Faecal Samples ◽  
Rrna Sequencing ◽  
Rectal Swabs ◽  
Neonates And Infants

Abstract Rectal swabs are potentially a valuable method for monitoring the gut microbiome in research and clinical settings, where it is important to adhere to strict timing, or where acute sampling is needed. It is currently unknown whether rectal swabs give comparable results to faecal samples regarding microbiota community composition in neonates and infants. To study how well the two sampling methods correlate in infants, we compared the 16S-rRNA-based sequencing results of 131 paired rectal swabs and faecal samples collected from 116 infants at two timepoints in early life. The paired samples were highly comparable regarding both diversity and overall community composition, and strongly correlated on taxonomical level. We observed no significant nor relevant contribution of sampling method to the variation in overall gut microbiota community composition in a multivariable model. Our study provides evidence supporting the use of rectal swabs as a reliable proxy for faecal samples in infant gut microbiota research.

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