scholarly journals The Species-Level Composition of the Fecal Bifidobacterium and Lactobacillus Genera in Indonesian Children Differs from That of Their Mothers

2021 ◽  
Vol 9 (9) ◽  
pp. 1995
Author(s):  
Mengfan Ding ◽  
Bo Yang ◽  
Wei Wei Thwe Khine ◽  
Yuan-Kun Lee ◽  
Endang Sutriswati Rahayu ◽  
...  
Keyword(s):  
Breast Milk ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Critical Role ◽  
Species Level ◽  
Bacterial Composition ◽  
Infant Feces ◽  
Relative Abundances ◽  
One Year

The infant gut microbiota plays a critical role in early life growth and derives mainly from maternal gut and breast milk. This study aimed to analyze the differences in the gut microbiota, namely Bifidobacterium and Lactobacillus communities at species level among breast milk as well as maternal and infant feces at different time points after delivery. Fifty-one mother–infant pairs from Indonesia were recruited, and the breast milk and maternal and infant feces were collected and analyzed by high throughput sequencing (16S rRNA, Bifidobacterium groEL and Lactobacillus groEL genes). PCoA results showed bacterial composition was different among breast milk and maternal and infant feces within the first two years. The abundance of Bifidobacterium and Bacteroides were significantly higher in infant feces compared to their maternal feces from birth to two years of age, and maternal breast milk within six months after birth (p < 0.05), whereas the abundance of Blautia, Prevotella, and Faecalibacterium was higher in maternal feces compared to that in breast milk within six months and infant feces within one year after birth, respectively (p < 0.05). The relative abundances of Bacteroides and Lactobacillus was higher and lower in infant feces compared to that in maternal feces only between one and two years of age, respectively (p < 0.05). For Bifidobacterium community at species level, B. adolescentis, B. ruminantium, B. longum subsp. infantis, B. bifidum, and B. pseudolongum were identified in all samples. However, the profile of Bifidobacterium was different between maternal and infant feces at different ages. The relative abundances of B. adolescentis and B. ruminantium were higher in maternal feces compared to those in infant feces from birth to one year of age (p < 0.05), while the relative abundances of B. longum subsp. infantis and B. bifidum were higher in infant feces compared to those in maternal feces beyond three months, and the relative abundance of B. pseudolongum was only higher in infant feces between three and six months (p < 0.05). For Lactobacillus community, L. paragasseri showed higher relative abundance in infant feces when the infant was younger than one year of age (p < 0.05). This study showed bacterial composition at the genus level and Bifidobacterium and Lactobacillus communities at the species level were stage specific in maternal breast milk as well as and maternal and infant feces.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

2021 ◽  
Vol 17 ◽  
pp. 117693432199635
Author(s):  
Daoxin Liu ◽  
Pengfei Song ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Zhenyuan Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Bacterial Phyla ◽  
In Captivity ◽  
Relative Abundances ◽  
Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

scholarly journals Heat stress affects fecal microbial and metabolic alterations of primiparous sows during late gestation

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jianwen He ◽  
Huiduo Guo ◽  
Weijiang Zheng ◽  
Yongqiang Xue ◽  
Ruqian Zhao ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Tricarboxylic Acid Cycle ◽  
Intestinal Barrier ◽  
Metabolic Changes ◽  
Late Gestation ◽  
Large White ◽  
Β Diversity

Abstract Background Heat stress (HS) jeopardizes intestinal barrier functions and augments intestinal permeability in pigs. However, whether HS-induced maternal microbial and metabolic changes in primiparous sows during late gestation remains elusive. We present here, a study investigating the fecal microbial and metabolic responses in late gestational primiparous sows when exposed to HS. Methods Twelve first-parity Landrace × Large White F1 sows were randomly assigned into two environmental treatments including the thermoneutral (TN) (18–22 °C; n = 6) and HS (28–32 °C; n = 6) conditions. Both treatments were applied from 85 d of gestation to farrowing. The serum and feces samples were collected on d 107 of gestation, for analyses including intestinal integrity biomarkers, high-throughput sequencing metagenomics, short-chain fatty acid (SCFA) profiles and nontargeted metabolomics. Results Our results show that HS group has higher serum Heat shock protein 70 (HSP70), lipopolysaccharide (LPS) and lipopolysaccharide-binding protein (LBP) levels. The gut microbial community can be altered upon HS by using β-diversity and taxon-based analysis. In particular, the relative abundance of genera and operational taxonomic units (OTUs) related to Clostridiales and Halomonas are higher in HS group, the relative abundance of genera and OTUs related to Bacteroidales and Streptococcus, however, are lower in HS group. Results of metabolic analysis reveal that HS lowers the concentrations of propionate, butyrate, total SCFA, succinate, fumarate, malate, lactate, aspartate, ethanolamine, β-alanine and niacin, whereas that of fructose and azelaic acid are higher in HS group. These metabolites mainly affect propanoate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine metabolism, β-alanine metabolism, pantothenate and CoA biosynthesis, tricarboxylic acid cycle (TCA) and nicotinate and nicotinamide metabolism. Additionally, correlation analysis between significant microbes and metabolites indicated that the HS-induced microbiota shift is likely the cause of changes of intestinal metabolism. Conclusions Taken together, we reveal characteristic structural and metabolic changes in maternal gut microbiota as a result of late gestational HS, which could potentially provide the basis for further study on offspring gut microbiota and immune programming.

scholarly journals Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients

2021 ◽  
Author(s):  
Xinyue Zhang ◽  
Kun Guo ◽  
Linjing Shi ◽  
Ting Sun ◽  
Songmei Geng
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Interleukin 2 ◽  
Negative Relationship ◽  
Healthy Individuals ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
The Relationship

Abstract Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease.Results: We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the dialister. The relative abundance of Phascolarctobacterium and dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions: We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.

scholarly journals Longitudinal Multi-Omics Study of a Mother-Infant Dyad from Breastfeeding to Weaning: An Individualized Approach to Understand the Interactions Among Diet, Fecal Metabolome and Microbiota Composition

2021 ◽  
Vol 8 ◽  
Author(s):  
Giorgia Conta ◽  
Federica Del Chierico ◽  
Sofia Reddel ◽  
Federico Marini ◽  
Fabio Sciubba ◽  
...  
Keyword(s):  
Breast Milk ◽  
Gut Microbiota ◽  
Single Mother ◽  
Critical Role ◽  
Short Chain Fatty Acids ◽  
Lactation Period ◽  
Common Component ◽  
Sequence Of Events ◽  
16S Rna ◽  
Stool Samples

The development of the human gut microbiota is characterized by a dynamic sequence of events from birth to adulthood, which make the gut microbiota unique for everyone. Its composition and metabolism may play a critical role in the intestinal homeostasis and health. We propose a study on a single mother-infant dyad to follow the dynamics of an infant fecal microbiota and metabolome changes in relation to breast milk composition during the lactation period and evaluate the changes induced by introduction of complementary food during the weaning period. Nuclear Magnetic Resonance (NMR)-based metabolomics was performed on breast milk and, together with 16S RNA targeted-metagenomics analysis, also on infant stool samples of a mother-infant dyad collected over a period running from the exclusive breastfeeding diet to weaning. Breast milk samples and neonatal stool samples were collected from the 4th to the 10th month of life. Both specimens were collected from day 103 to day 175, while from day 219–268 only stool samples were examined. An exploratory and a predictive analysis were carried out by means of Common component and specific weight analysis and multi-block partial least squares discriminant analysis, respectively. Stools collected during breastfeeding and during a mixed fruit/breastfeeding diet were characterized by high levels of fucosyl-oligosaccharides and glycolysis intermediates, including succinate and formate. The transition to a semi-solid food diet was characterized by several changes in fecal parameters: increase in short-chain fatty acids (SCFAs) levels, including acetate, propionate and butyrate, dissapearance of HMOs and the shift in the community composition, mainly occurring within the Firmicutes phylum. The variations in the fecal metabolome reflected the infant’s diet transition, while the composition of the microbiota followed a more complex and still unstable behavior.

scholarly journals High-Throughput Absolute Quantification Sequencing Revealed Osteoporosis-Related Gut Microbiota Alterations in Han Chinese Elderly

2021 ◽  
Vol 11 ◽  
Author(s):  
Muhong Wei ◽  
Can Li ◽  
Yu Dai ◽  
Haolong Zhou ◽  
Yuan Cui ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Absolute Quantification ◽  
Osteoporosis Prevention ◽  
Mineral Density ◽  
Health Maintenance ◽  
Epidemiologic Evidence ◽  
Bacteroidetes Phylum ◽  
Relative Abundances ◽  
Ridge Regression Analysis

ObjectiveAccumulative evidence suggests that gut microbiota play an important role in bone remodeling and hence bone health maintenance. This study aimed to explore the association of gut microbiota with the risk of osteoporosis and to identify potential disease-related taxa, which may be promising targets in osteoporosis prevention and treatment in the future.MethodsAbsolute quantification 16S ribosomal RNA gene sequencing was used to detect absolute and relative abundances of gut microbiota in 44 patients with osteoporosis and 64 controls. In combination with one of our previous studies, a total of 175 samples were involved in the relative abundance analysis.ResultsCompared with the controls, the patients with osteoporosis had higher absolute and relative abundances of Bacteroidetes phylum, and Bacteroides and Eisenbergiella genera. The absolute abundances of Clostridium_XlVa, Coprococcus, Lactobacillus, and Eggerthella genera increased, and that of the Veillonella genus decreased in the osteoporosis group. As for relative abundance, that of the Parabacteroides and Flavonifractor genera increased, whereas that of the Raoultella genus decreased in the osteoporosis group. Controlling for potential confounders, the associations of Clostridium_XlVa, Coprococcus, and Veillonella genera with the risk of osteoporosis did not maintain significance. Ridge regression analysis suggested that Bacteroides is associated with reduced bone mineral density (BMD) and T-score at lumbar spines, and Anaerovorax is associated with increased BMD at the femoral neck. Functional predictions revealed that 10 Kyoto Encyclopedia of Genes and Genomes pathways were enriched in the osteoporosis group.ConclusionsGut microbiota compositions may contribute to the risk of osteoporosis. Several specific taxa and functional pathways are identified to associate with reduced bone density, thus providing epidemiologic evidence for the potential role of aberrant gut microbiota in osteoporosis pathogenesis.

scholarly journals metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effect models

2018 ◽  
Author(s):  
Nhan Thi Ho ◽  
Fan Li
Keyword(s):  
Random Effects ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
R Package ◽  
Standard Errors ◽  
Relative Abundances ◽  
Meta Analyses ◽  
Analysis Models

ABSTRACTBackgroundThe rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene amplicons are often preprocessed into composition or relative abundance. However, reproducibility has been lacking due to the myriad of different experimental and computational approaches taken in these studies. Microbiome studies may report varying results on the same topic, therefore, meta-analyses examining different microbiome studies to provide robust results are important. So far, there is still a lack of implemented methods to properly examine differential relative abundances of microbial taxonomies and to perform meta-analysis examining the heterogeneity and overall effects across microbiome studies.ResultsWe developed an R package ‘metamicrobiomeR’ that applies Generalized Additive Models for Location, Scale and Shape (GAMLSS) with a zero-inflated beta (BEZI) family (GAMLSS-BEZI) for analysis of microbiome relative abundance datasets. Both simulation studies and application to real microbiome data demonstrate that GAMLSS-BEZI well performs in testing differential relative abundances of microbial taxonomies. Importantly, the estimates from GAMLSS-BEZI are log(odds ratio) of relative abundances between groups and thus are comparable between microbiome studies. As such, we also apply random effects meta-analysis models to pool estimates and their standard errors across microbiome studies. We demonstrate the meta-analysis workflow and highlight the utility of our package on four studies comparing gut microbiomes between male and female infants in the first six months of life.ConclusionsGAMLSS-BEZI allows proper examination of microbiome relative abundance data. Random effects meta-analysis models can be directly applied to pool comparable estimates and their standard errors to evaluate the heterogeneity and overall effects across microbiome studies. The examples and workflow using our metamicrobiomeR package are reproducible and applicable for the analyses and meta-analyses of other microbiome studies.

scholarly journals ShenLing BaiZhu San alleviates Ulcerative Colitis in Rats by Regulating Gut Microbiota

2020 ◽  
Author(s):  
Daxing Gu ◽  
Shanshan Zhou ◽  
Lili Yao ◽  
Ying Tan ◽  
Xingzi Chi ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Rat Model ◽  
High Throughput Sequencing ◽  
Intestinal Barrier Function ◽  
Enzyme Linked Immunosorbent Assay ◽  
Trinitrobenzene Sulfonic Acid ◽  
Rrna Gene ◽  
Therapeutic Effects

Abstract Background: Recent studies have suggested that Shenling Baizhu San (SLBZS), an complementary and alternative medical therapy for ulcerative colitis (UC), alleviate clinic symptoms by the improvement of biochemical criteria and restoration of the intestinal barrier function. SLBZS as a famous Chinese herbal formula has been reportedly used to treat UC, of which mechanism is unknown. This study investigated the therapeutic effects of SLBZS on restoring the gut microbiota in a UC rat model. Methods: We proposed a 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced UC rat model to monitor the structural modulation of the gut microbiota. The test period was 10 days (observation for two days after modeling, treatment for 8 days by SLBZS). In this study, the level of inflammatory cytokines and activity of antioxidant enzymes in serum were ascertained by enzyme-linked immunosorbent assay (ELISA) and histological changes of colon were observed. Feces were collected for high-throughput sequencing of 16S rRNA gene. Results: SLBZS partly reduced the diversity of the gut microbiota, while the abundance of that is increased. Furthermore, at the genus level, the relative abundance of short chain fatty acids (SCFA) producing bacteria including Prevotella and Oscillospira increased, while the relative abundance of harmful bacteria including Desulfovibrio, and Bilophila decreased. Additionally, SLBZS could improve the lesions of colon and significantly reduce the expression of Interleukin-6 (IL-6) and Myeloperoxidase (MPO) and increase the activities of Superoxide dismutase (SOD) and Catalase (CAT) in rats serum. Conclusions: These results demonstrate that SLBZS may treat UC effectively by inhibiting inflammation, enhancing antioxidant capacity and regulating gut microbiota.

scholarly journals Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota

2020 ◽  
Author(s):  
Tuoyu He ◽  
Yun Jiang ◽  
Pengpeng Wang ◽  
Jianguo Xiang ◽  
Wangcheng Pan
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Skin Disease ◽  
High Throughput Sequencing ◽  
Health Conditions ◽  
Microbiota Composition ◽  
Significant Difference ◽  
Host Health ◽  
Host Diet ◽  
Gut Microbiota Composition

AbstractThe composition and abundance of gut microbiota is essential for host health and immunity. Gut microbiota is symbiotic with the host, so changes in the host diet, development, and health will lead to changes in the gut microbiota. Conversely, changes in the gut microbiota also affect the host conditions. In this experiment, 16S rRNA high-throughput sequencing was used to compare the gut microbiota composition of 5 healthy Paa Spinosa and 6 P. spinosa with rotten-skin disease. Results: the gut microbiota composition was significant difference between diseased P. spinosa and the healthy P. spinosa; LEfSe analysis showed that the relative abundance of Methanocorpusculum, Parabacteroides, AF12, PW3, Epulopiscium, and Oscillospira were significantly higher in the diseased P. spinosa, while the relative abundance of Serratia, Eubacteium, Citrobacter, and Morganella were significantly lower. Conclusion: Rotten-skin disease changed P. spinosa gut microbiota significantly; The relative abundance of Epulopiscium and Oscillospira might be related to the health conditions of the host skin and gallbladder; The relative abundance of Serratia and Eubacteium might be important for maintaining the gut microbiota ecosystem.

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