Temporal dynamics of the gut microbiome and metabolome in preterm and term infants from birth through the first year of life

2020 ◽  
Author(s):  
Polly Soo Xi Yap ◽  
Chun Wie Chong ◽  
Azanna Ahmad Kamar ◽  
Ivan Kok Seng Yap ◽  
Yao Mun Choo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Preterm Infants ◽  
Pathogenic Bacteria ◽  
Mode Of Delivery ◽  
Preterm Neonates ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Distinct Level

Abstract Background: Emerging evidence has shown a link between the perturbations and development of the gut microbiota in infants to their immediate and long-term health. In comparison to the healthy full-term neonate, preterm neonates experience disparate gut bacterial establishment (e.g. duration in the womb), colonisation (e.g. mode of delivery), and development (e.g. frequent use of antibiotics). To better understand the assembly of the gut microbiota in preterm infants, faecal samples were longitudinally collected from preterm (n = 19) and term (n = 20) infants, up to 12 months after birth. We characterised bacterial compositions by 16S rRNA gene sequencing (n = 141) and metabolomics profiling (n = 141) using nuclear magnetic resonance (NMR) spectroscopy.Results: Significant differences in faecal bacterial composition between term and preterm infants were detected in sample collected in week 2, month 6 and month 12. Interestingly, separation of the bacterial composition between term and preterm infants was more pronounced at month 12 as compared to the earlier time-points, suggesting distinct level of microbial maturation in gut between the two groups. Intestinal microbiota of preterm neonates was consistently characterised by dominance of pathogenic bacteria from the Enterobacteriaceae family and a paucity of strictly anaerobic taxa including Veillonella and Bacteroides relative to infants born at term. Consistent result was observed in the stool NMR spectroscopy in which clear separation in stool metabolomics profiles was observed between the term and preterm neonates.Conclusion: Overall, we identified a panel of amino acid metabolites and central metabolism intermediates in the preterm infants’ stool, possibly indicating incomplete fermentation of complex polysaccharides in the guts of these infants. In contrast, the term infant stool had significantly higher levels of metabolites which are commonly found in milk such as fucose and β-hydroxybutyrate (BHBA). Birth weight was selected as the best explanatory variable for the metabolomics profiles, pointing to the strong relationship between protein synthesis, as well as fucose and BHBA in physical development. By following both term and preterm infants for 12 months, our study reported the dynamic of gut microbial composition and their contribution to metabolism and potential impact to growth in neonates.

scholarly journals Neonatal intensive care unit (NICU) exposures exert a sustained influence on the progression of gut microbiota and metabolome in the first year of life

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Polly Soo Xi Yap ◽  
Chun Wie Chong ◽  
Azanna Ahmad Kamar ◽  
Ivan Kok Seng Yap ◽  
Yao Mun Choo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Preterm Infants ◽  
Neonatal Intensive Care ◽  
Early Time ◽  
16S Rrna Gene Sequencing ◽  
Resonance Spectroscopy ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Term Infants ◽  
Rrna Gene Sequencing

AbstractEmerging evidence has shown a link between the perturbations and development of the gut microbiota in infants with their immediate and long-term health. To better understand the assembly of the gut microbiota in preterm infants, faecal samples were longitudinally collected from the preterm (n = 19) and term (n = 20) infants from birth until month 12. 16S rRNA gene sequencing (n = 141) and metabolomics profiling (n = 141) using nuclear magnetic resonance spectroscopy identified significant differences between groups in various time points. A panel of amino acid metabolites and central metabolism intermediates significantly correlated with the relative abundances of 8 species of bacteria were identified in the preterm group. In contrast, faecal metabolites of term infants had significantly higher levels of metabolites which are commonly found in milk such as fucose and β-hydroxybutyrate. We demonstrated that the early-life factors such as gestational age, birth weight and NICU exposures, exerted a sustained effect to the dynamics of gut microbial composition and metabolism of the neonates up to one year of age. Thus, our findings suggest that intervention at this early time could provide ‘metabolic rescue’ to preterm infants from aberrant initial gut microbial colonisation and succession.

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

Life ◽  
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.

scholarly journals Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Camilo Quiroga-González ◽  
Luis Alberto Chica Cardenas ◽  
Mónica Ramírez ◽  
Alejandro Reyes ◽  
Camila González ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Site Conditions ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Diet Diversity ◽  
Woolly Monkeys ◽  
The Moment ◽  
Positive Effect ◽  
Lagothrix Lagothricha

AbstractMicrobiome is known to play an important role in the health of organisms and different factors such as diet have been associated with modifications in microbial communities. Differences in the microbiota composition of wild and captive animals has been evaluated; however, variation during a reintroduction process in primates has never been reported. Our aim was to identify changes in the bacterial composition of three individuals of reintroduced woolly monkeys (Lagothrix lagothricha) and the variables associated with such changes. Fecal samples were collected and the V4 region of the 16S rRNA gene was sequenced to determine gut microbial composition and functionality. Individual samples from released individuals showed a higher microbial diversity after being released compared to before liberation, associated with changes in their diet. Beta diversity and functionality analysis showed separation of samples from released and captive conditions and the major factor of variation was the moment of liberation. This study shows that intestinal microbiota varies depending on site conditions and is mainly associated with diet diversity. The intake of food from wild origin by released primates may promote a positive effect on gut microbiota, improving health, and potentially increasing success in reintroduction processes.

scholarly journals First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lampet Wongsaroj ◽  
Ratmanee Chanabun ◽  
Naruemon Tunsakul ◽  
Pinidphon Prombutara ◽  
Somsak Panha ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Organic Fertilizer ◽  
The Other ◽  
Organic Fertilizers ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Physiochemical Properties ◽  
Nutrient Profiles ◽  
Soil Recovery ◽  
Local Farmers

AbstractNortheastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson’s correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.

scholarly journals The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota

2021 ◽  
Vol 9 (2) ◽  
pp. 278
Author(s):  
Shen Jean Lim ◽  
Miriam Aguilar-Lopez ◽  
Christine Wetzel ◽  
Samia V. O. Dutra ◽  
Vanessa Bray ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Preterm Infant ◽  
Neonatal Intensive Care ◽  
Genetic Relatedness ◽  
Bovine Milk ◽  
Alpha Diversity ◽  
Neonatal Intensive Care Units ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Operational Taxonomic Units

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

scholarly journals Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China

2020 ◽  
Vol 10 ◽  
Author(s):  
Xun Kang ◽  
Yanhong Wang ◽  
Siping Li ◽  
Xiaomei Sun ◽  
Xiangyang Lu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Disease Control ◽  
Bacterial Communities ◽  
Mosquito Species ◽  
Microbial Community Composition ◽  
Variable Region ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Quality Filtering ◽  
And Function

The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3−V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.

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

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.

scholarly journals Altered Fecal Metabolites and Colonic Glycerophospholipids Were Associated With Abnormal Composition of Gut Microbiota in a Depression Model of Mice

2021 ◽  
Vol 15 ◽  
Author(s):  
Xue Gong ◽  
Cheng Huang ◽  
Xun Yang ◽  
Jianjun Chen ◽  
Juncai Pu ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Underlying Mechanism ◽  
Rrna Gene ◽  
Mice Model ◽  
Microbial Composition ◽  
Gas And Liquid Chromatography ◽  
Correlation Analysis Method ◽  
Rrna Gene Sequencing

The microbiota–gut–brain axis has been considered to play an important role in the development of depression, but the underlying mechanism remains unclear. The gastrointestinal tract is home to trillions of microbiota and the colon is considered an important site for the interaction between microbiota and host, but few studies have been conducted to evaluate the alterations in the colon. Accordingly, in this study, we established a chronic social defeated stress (CSDS) mice model of depression. We applied 16S rRNA gene sequencing to assess the gut microbial composition and gas and liquid chromatography–mass spectroscopy to identify fecal metabolites and colonic lipids, respectively. Meanwhile, we used Spearman’s correlation analysis method to evaluate the associations between the gut microbiota, fecal metabolites, colonic lipids, and behavioral index. In total, there were 20 bacterial taxa and 18 bacterial taxa significantly increased and decreased, respectively, in the CSDS mice. Further, microbial functional prediction demonstrated a disturbance of lipid, carbohydrate, and amino acid metabolism in the CSDS mice. We also found 20 differential fecal metabolites and 36 differential colonic lipids (in the category of glycerolipids, glycerophospholipids, and sphingolipids) in the CSDS mice. Moreover, correlation analysis showed that fecal metabolomic signature was associated with the alterations in the gut microbiota composition and colonic lipidomic profile. Of note, three lipids [PC(16:0/20:4), PG(22:6/22:6), and PI(18:0/20:3), all in the category of glycerophospholipids] were significantly associated with anxiety- and depression-like phenotypes in mice. Taken together, our results indicated that the gut microbiota might be involved in the pathogenesis of depression via influencing fecal metabolites and colonic glycerophospholipid metabolism.

scholarly journals Exploring the role of gut microbiota in host feeding behavior among breeds in swine

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Yuqing He ◽  
Francesco Tiezzi ◽  
Jeremy Howard ◽  
Yijian Huang ◽  
Kent Gray ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Feeding Behavior ◽  
Growth Stages ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Host Feeding ◽  
Microbial Composition ◽  
Large White ◽  
Rrna Gene Sequencing ◽  
Host Metabolism

Abstract Background The interplay between the gut microbiota and feeding behavior has consequences for host metabolism and health. The present study aimed to explore gut microbiota overall influence on feeding behavior traits and to identify specific microbes associated with the traits in three commercial swine breeds at three growth stages. Feeding behavior measures were obtained from 651 pigs of three breeds (Duroc, Landrace, and Large White) from an average 73 to 163 days of age. Seven feeding behavior traits covered the information of feed intake, feeder occupation time, feeding rate, and the number of visits to the feeder. Rectal swabs were collected from each pig at 73 ± 3, 123 ± 4, and 158 ± 4 days of age. DNA was extracted and subjected to 16 S rRNA gene sequencing. Results Differences in feeding behavior traits among breeds during each period were found. The proportion of phenotypic variances of feeding behavior explained by the gut microbial composition was small to moderate (ranged from 0.09 to 0.31). A total of 21, 10, and 35 amplicon sequence variants were found to be significantly (q-value < 0.05) associated with feeding behavior traits for Duroc, Landrace, and Large White across the three sampling time points. The identified amplicon sequence variants were annotated to five phyla, with Firmicutes being the most abundant. Those amplicon sequence variants were assigned to 28 genera, mainly including Christensenellaceae_R-7_group, Ruminococcaceae_UCG-004, Dorea, Ruminococcaceae_UCG-014, and Marvinbryantia. Conclusions This study demonstrated the importance of the gut microbial composition in interacting with the host feeding behavior and identified multiple archaea and bacteria associated with feeding behavior measures in pigs from either Duroc, Landrace, or Large White breeds at three growth stages. Our study provides insight into the interaction between gut microbiota and feeding behavior and highlights the genetic background and age effects in swine microbial studies.

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.

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