scholarly journals Diversity structure of the microbial communities in the guts of four neotropical termite species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10959
Author(s):  
Surendra Vikram ◽  
Joel D. Arneodo ◽  
Javier Calcagno ◽  
Maximiliano Ortiz ◽  
Maria Laura Mon ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Feeding Habits ◽  
Termite Species ◽  
Structure Comparison ◽  
Β Diversity ◽  
Nasutitermes Corniger ◽  
Α Diversity ◽  
Termite Gut ◽  
Microbial Community Assembly ◽  
Feeding Sources

The termite gut microbiome is dominated by lignocellulose degrading microorganisms. This study describes the intestinal microbiota of four Argentinian higher termite species with different feeding habits: Microcerotermes strunckii (hardwood), Nasutitermes corniger (softwood), Termes riograndensis (soil organic matter/grass) and Cornitermes cumulans (grass) by deep sequencing of amplified 16S rRNA and ITS genes. In addition, we have performed a taxonomic and gut community structure comparison incorporating into the analysis the previously reported microbiomes of additional termite species with varied diets. The bacterial phylum Spirochaetes was dominant in the guts of M. strunckii, N. corniger and C. cumulans, whereas Firmicutes predominated in the T. riograndensis gut microbiome. A single bacterial genus, Treponema (Spirochaetes), was dominant in all termite species, except for T. riograndensis. Both in our own sequenced samples and in the broader comparison, prokaryotic α-diversity was higher in the soil/grass feeders than in the wood feeders. Meanwhile, the β-diversity of prokaryotes and fungi was highly dissimilar among strict wood-feeders, whereas that of soil- and grass-feeders grouped more closely. Ascomycota and Basidiomycota were the only fungal phyla that could be identified in all gut samples, because of the lack of reference sequences in public databases. In summary, higher microbial diversity was recorded in termites with more versatile feeding sources, providing further evidence that diet, along with other factors (e.g., host taxonomy), influences the microbial community assembly in the termite gut.

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

scholarly journals Gut microbiome as a response marker for pancreatic enzyme replacement therapy in a porcine model of exocrine pancreas insufficiency

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Sabrina Ritz ◽  
Daniela Hahn ◽  
Haleluya T. Wami ◽  
Karin Tegelkamp ◽  
Ulrich Dobrindt ◽  
...  
Keyword(s):  
Enzyme Replacement Therapy ◽  
Replacement Therapy ◽  
Gut Microbiome ◽  
Pancreatic Enzyme ◽  
Microbial Composition ◽  
Enzyme Replacement ◽  
Β Diversity ◽  
Healthy State ◽  
Α Diversity ◽  
Pancreatic Enzyme Replacement Therapy

Abstract Background Exocrine pancreatic insufficiency (EPI) is characterized by the loss of active pancreatic enzymes and a resulting severely reduced food digestion. EPI therapy requires orally applied pancreatic enzyme replacement. The gut microbiome is a known mediator of intestinal diseases and may influence the outcome of EPI and the effects of a pancreatic enzyme replacement therapy (PERT). Here, we analyzed the effects of EPI and PERT on the gut microbiome in the model of pancreatic duct ligated minipigs. Results The microbial community composition in pig feces was analyzed by next generation sequencing of 16S rRNA amplicons. The data were evaluated for α- and β-diversity changes and changes at the different Operational Taxonomic Unit (OTU) levels by Shannon–Wiener and inverse Simpson index calculation as well as by Principal Coordinates Analysis based on Bray–Curtis dissimilarity. Microbial α-diversity was reduced after EPI induction and reverted to nearly healthy state after PERT. Analysis of microbial composition and β-diversity showed distinctive clusters of the three study groups and a change towards a composition comparable to healthy animals upon PERT. The relative abundance of possible pathobionts like Escherichia/Shigella, Acinetobacter or Stenotrophomonas was reduced by PERT. Conclusion These data demonstrate that EPI-induced dysbiosis could be reverted by PERT to a nearly healthy state. Elevated α-diversity and the reduction of bacterial overgrowth after PERT promises benefits for EPI patients. Non-invasive microbiome studies may be useful for EPI therapy monitoring and as marker for response to PERT.

scholarly journals The Effect of Probiotics Supplementation on the Gut Microbiome of Healthy Dogs Assessed Using Metagenomic Sequencing: A Randomized Control Trial

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1591-1591
Author(s):  
Jirayu Tanprasertsuk ◽  
Justin Shmalberg ◽  
Aashish Jha ◽  
LeeAnn Perry ◽  
Ryan Honaker
Keyword(s):  
Health Outcomes ◽  
Gut Microbiome ◽  
Randomized Control Trial ◽  
Gastrointestinal Diseases ◽  
Metagenomic Sequencing ◽  
Β Diversity ◽  
Α Diversity ◽  
Stool Samples ◽  
Healthy Dogs ◽  
Randomized Control

Abstract Objectives Dogs share similar gut microbiome (GM) with humans, making them a great model for investigating the effects of probiotics (PR) on GM and health. This randomized control trial examined changes in MB and health outcomes in household dogs after PR supplementation. Methods All dogs recruited were fed human grade cooked food ≥ 1 mo, not fed any cultured food, PR, prebiotics, or on antibiotics ≥ 3 mo, and absent of major diseases. Dogs were randomized to receive a daily dose of PR (20 billion CFU of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples at baseline and 4 weeks after the intervention in both groups. Additional stool samples were collected 2 weeks after stopping the PR in the PR group. GM profiling was performed with metagenomic sequencing. Results Twenty three dogs in the PR and 19 dogs in the PL group completed the trial (5.6 ± 3.0 y, 69% male). PR had no effect on α-diversity. As compared to baseline, changes in β-diversity at the species level in 4.3% of GM were significantly affected by PR at week 4 (P < 0.001) but not at week 6. A significant increase (adj P < 0.01) for ≥ 2-fold in abundance was observed at week 4 as compared to baseline for 41 bacterial taxa, 29 (71%) of which belong in the Lactobacillus genus. The abundance of E. coli also decreased at week 4 in the PR group (2.8 folds, adj P < 0.01). The abundance of these taxa returned to baseline at week 6. Such changes in diversity or abundance were not observed with PL. Dogs fed PR tended to be at a lower risk of diarrhea during the trial (0% vs 16%, P = 0.08). No change in other health outcomes was observed. Conclusions Oral PR supplementation has a small but significant effect on GM in healthy dogs. Findings warrant further investigation with longer duration in populations at a higher risk of gastrointestinal diseases. Funding Sources NomNomNow Inc.

scholarly journals Fecal Microbiota Composition of a Mother-Infant Dyad in a Pig Model

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1015-1015
Author(s):  
Julie Jeon ◽  
Xi Fang ◽  
Jeferson Lourenco ◽  
Srujana Rayalam ◽  
Michael Rothrock ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Maternal Nutrition ◽  
Early Stage ◽  
Illumina Miseq ◽  
Well Being ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Gut Health ◽  
Β Diversity ◽  
Α Diversity

Abstract Objectives Microbial programming in early life is associated with gut health and overall well-being in adulthood. The establishment of the nascent gut microbiome is substantially influenced by both maternal nutrition and the native maternal microbiome. Pig is recognized as a valuable model in gastrointestinal track research due to its remarkable similarity to humans in gastrointestinal anatomy, physiology, biochemistry, immunology, and pathology. This study examined the characteristics of the gut microflora in the sow-piglet dyad. Methods Fecal samples were collected from sows (n = 6) and piglets (n = 24) at weaning. Bacterial DNA was isolated from the feces and the V3-V4 region of 16 s rRNA gene was amplified and sequenced using the Illumina Miseq platform and analyzed by QIIME pipeline. Results Sows had a twice higher abundance of Firmicutes than piglets (84.28% vs 40.19%, P < 0.0001), although Firmicutes was the most abundant phyla in both sows and piglets. Instead, piglets had higher abundances of Bacteroidetes (36.41% vs 9.61%, P < 0.0001) and Proteobacteria (11.31% vs 0.87%, P = 0.005) than sows. Early colonization of Proteobacteria has been suggested to be important for development of neonatal immunity. Firmicutes to Bacteroidetes ratio was higher in sows than in piglets (16.32 vs 1.36, P < 0.0001), which is consistent with previous reports in humans. The five most abundant families in sows were Clostridiaceae (30.43%), Turicibacteraceae (17.13%), Ruminococcaceae (11.29%), Lactobacillaceae (8.27%), and Lachnospiraceae (4.99%), while those in piglets were Bacteroidaceae (23.96%), Lachnospiraceae (9.13%), Clostridiaceae (7.52%), Ruminococcaceae (6.80%), and Enterobacteriaceae (6.63%). Observed OTUs in sows were higher (P = 0.02) than those in piglets, suggesting that piglets at early stage of life have lower fecal α-diversity. Moreover, β-diversity was very different between sows and piglets (P = 0.01). Conclusions Sows and piglets showed distinctive pattern of fecal microflora, and piglets had fewer species numbers at weaning compared to that of sows. This finding will provide a valuable information for future transgenerational studies on the gut microbiome and its consequences for health using a sow-piglet dyad. Funding Sources Georgia Experimental Agricultural Station, UGA Faculty research grant, and Center for Chronic Disorders of Aging at the PCOM.

scholarly journals Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus–Exposed, Uninfected Infants

2019 ◽  
Vol 71 (11) ◽  
pp. 2858-2868 ◽  
Author(s):  
Alaric W D’Souza ◽  
Eshia Moodley-Govender ◽  
Bertram Berla ◽  
Tejas Kelkar ◽  
Bin Wang ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Gut Microbiome ◽  
Cotrimoxazole Prophylaxis ◽  
Β Diversity ◽  
Α Diversity ◽  
Immunodeficiency Virus ◽  
Functional Pathway ◽  
Exposed Uninfected

Abstract Background Prophylactic cotrimoxazole treatment is recommended in human immunodeficiency virus (HIV)–exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined. Methods We analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n = 34; CTX-T) or to not receive (n = 29; CTX-N) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between the CTX-T and CTX-N infants. Results Metagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T and CTX-N infants. In contrast, resistance gene prevalence (P = .00719) and α-diversity (P = .0045) increased in CTX-T infants. These differences increased over time for both resistance gene prevalence measured by log-normalized abundance (4-month mean, 0.71 [95% confidence interval {CI}, .2–1.2] and 6-month mean, 0.85 [95% CI, .1–1.7]) and α-diversity (P = .0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean, −0.11 [95% CI, −.15 to −.077]), functional taxonomic (mean, −0.050 [95% CI, −.084 to −.017]), and resistance gene (mean, −0.13 [95% CI, −.17 to −.099]) β-diversity decreased in CTX-T infants compared with CTX-N infants. These results are consistent with persistent antibiotic selection pressure. Conclusions Cotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.

scholarly journals Vitamin D Metabolites and the Gut Microbiome in Older Men

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 840-840
Author(s):  
Deborah Kado ◽  
Robert Thomas ◽  
Lingjing Jiang ◽  
John Adams ◽  
Rob Knight ◽  
...  
Keyword(s):  
Vitamin D ◽  
Gut Microbiome ◽  
Forest Plot ◽  
Vitamin D Metabolites ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Α Diversity ◽  
Unweighted Unifrac ◽  
Antidepressant Use

Abstract We examined the bidirectional impact of vitamin D on the composition and diversity of the gut microbiome in 567 MrOS men. Vitamin D metabolites were measured using LC-MSMS and stool sub-operational taxonomic units defined from 16S ribosomal RNA sequencing data using Deblur and Greengenes 13.8. Men’s mean serum level of 25(OH)D was in the sufficient range. Faith’s Phylogenetic Diversity and non-redundant covariate analyses revealed that 1,25(OH)2D explained 5% of variance in α-diversity; the other non-redundant covariates of site, race, recent antibiotic and antidepressant use explained another 6%. In β-diversity analyses using unweighted UniFrac, 1,25(OH)2D was the strongest factor assessed, explaining 2%. Random forest plot analyses identified 12 taxa, 6 in the phylum Firmicutes, positively associated with either 1,25(OH)2D and/or [1,25(OH)2D/25(OH)D] activation ratio. Higher levels of the active 1,25(OH)2D, but not 25(OH)D, were associated with butyrate producing bacteria. Men with favorable vitamin D activation profiles also had greater gut microbial diversity.

scholarly journals Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study

2021 ◽  
Vol 17 ◽  
pp. 117693432110575
Author(s):  
Peidong Yang ◽  
Zhitang Wang ◽  
Qingqin Peng ◽  
Weibin Lian ◽  
Debo Chen
Keyword(s):  
Breast Cancer ◽  
Breast Carcinoma ◽  
Gut Microbiota ◽  
Malignant Tumor ◽  
Gut Microbiome ◽  
Benign Tumor ◽  
Β Diversity ◽  
Tumor Group ◽  
Α Diversity ◽  
Malignant Breast

The microbiome plays diverse roles in many diseases and can potentially contribute to cancer development. Breast cancer is the most commonly diagnosed cancer in women worldwide. Thus, we investigated whether the gut microbiota differs between patients with breast carcinoma and those with benign tumors. The DNA of the fecal microbiota community was detected by Illumina sequencing and the taxonomy of 16S rRNA genes. The α-diversity and β-diversity analyses were used to determine richness and evenness of the gut microbiota. Gene function prediction of the microbiota in patients with benign and malignant carcinoma was performed using PICRUSt. There was no significant difference in the α-diversity between patients with benign and malignant tumors ( P = 3.15e−1 for the Chao index and P = 3.1e−1 for the ACE index). The microbiota composition was different between the 2 groups, although no statistical difference was observed in β-diversity. Of the 31 different genera compared between the 2 groups, level of only Citrobacter was significantly higher in the malignant tumor group than that in benign tumor group. The metabolic pathways of the gut microbiome in the malignant tumor group were significantly different from those in benign tumor group. Furthermore, the study establishes the distinct richness of the gut microbiome in patients with breast cancer with different clinicopathological factors, including ER, PR, Ki-67 level, Her2 status, and tumor grade. These findings suggest that the gut microbiome may be useful for the diagnosis and treatment of malignant breast carcinoma.

scholarly journals The Gut Microbiome of Heart Failure With Preserved Ejection Fraction

2021 ◽  
Author(s):  
Anna L. Beale ◽  
Joanne A. O’Donnell ◽  
Michael E. Nakai ◽  
Shane Nanayakkara ◽  
Donna Vizi ◽  
...  
Keyword(s):  
Risk Factors ◽  
Heart Failure ◽  
Ejection Fraction ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Short Chain ◽  
Preserved Ejection Fraction ◽  
Β Diversity ◽  
Α Diversity ◽  
Significant Difference

Background Risk factors for heart failure with preserved ejection fraction (HFpEF) include hypertension, age, sex, and obesity. Emerging evidence suggests that the gut microbiota independently contributes to each one of these risk factors, potentially mediated via gut microbial‐derived metabolites such as short‐chain fatty acids. In this study, we determined whether the gut microbiota were associated with HFpEF and its risk factors. Methods and Results We recruited 26 patients with HFpEF and 67 control participants from 2 independent communities. Patients with HFpEF were diagnosed by exercise right heart catheterization. We assessed the gut microbiome by bacterial 16S rRNA sequencing and food intake by the food frequency questionnaire. There was a significant difference in α‐diversity (eg, number of microbes) and β‐diversity (eg, type and abundance of microbes) between both cohorts of controls and patients with HFpEF ( P =0.001). We did not find an association between β‐diversity and specific demographic or hemodynamic parameters or risk factors for HFpEF. The Firmicutes to Bacteroidetes ratio, a commonly used marker of gut dysbiosis, was lower, but not significantly so ( P =0.093), in the patients with HFpEF. Compared with controls, the gut microbiome of patients with HFpEF was depleted of bacteria that are short‐chain fatty acid producers. Consistent with this, participants with HFpEF consumed less dietary fiber (17.6±7.7 versus 23.2±8.8 g/day; P =0.016). Conclusions We demonstrate key changes in the gut microbiota in patients with HFpEF, including the depletion of bacteria that generate metabolites known to be important for cardiovascular homeostasis. Further studies are required to validate the role of these gut microbiota and metabolites in the pathophysiology of HFpEF.

scholarly journals Host Factors Affect the Gut Microbiome More Significantly than Diet Shift

2021 ◽  
Vol 9 (12) ◽  
pp. 2520
Author(s):  
Enkhchimeg Lkhagva ◽  
Hea-Jong Chung ◽  
Ji-Seon Ahn ◽  
Seong-Tshool Hong
Keyword(s):  
Physical Exercise ◽  
Gut Microbiome ◽  
Theoretical Basis ◽  
Host Factors ◽  
Diet Shift ◽  
Β Diversity ◽  
Α Diversity ◽  
Determining Factors ◽  
Vegetarian Diets ◽  
Current Science

The determining factors of the composition of the gut microbiome are one of the main interests in current science. In this work, we compared the effect of diet shift (DS) from heavily relying on meatatarian diets to vegetarian diets and physical exercise (EX) on the composition of the gut microbiome after 3 months. Although both DS and EX affected the composition of the gut microbiome, the patterns of alteration were different. The α-diversity analyzed by InvSimpson, Shannon, Simpson, and Evenness showed that both EX and DS affected the microbiome, causing it to become more diverse, but EX affected the gut microbiome more significantly than DS. The β-diversity analyses indicated that EX and DS modified the gut microbiome in two different directions. Co-occurrence network analysis confirmed that both EX and DS modified the gut microbiome in different directions, although EX modified the gut microbiome more significantly. Most notably, the abundance of Dialister succinatiphilus was upregulated by EX, and the abundances of Bacteroides fragilis, Phascolarctobacterium faecium, and Megasphaera elsdenii were downregulated by both EX and DS. Overall, EX modulated the composition of the gut microbiome more significantly than DS, meaning that host factors are more important in determining the gut microbiome than diets. This work also provides a new theoretical basis for why physical exercise is more health-beneficial than vegetarian diets.

scholarly journals Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance

2021 ◽  
Vol 9 (7) ◽  
pp. 1490
Author(s):  
Camila E. Orsso ◽  
Ye Peng ◽  
Edward C. Deehan ◽  
Qiming Tan ◽  
Catherine J. Field ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Species Richness ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Pediatric Obesity ◽  
Model Assessment ◽  
Shotgun Metagenomics ◽  
Β Diversity ◽  
Diversity Measures ◽  
Α Diversity

The gut microbiome is hypothesized to play a crucial role in the development of obesity and insulin resistance (IR); the pathways linking the microbiome to IR in pediatrics have yet to be precisely characterized. We aimed to determine the relationship between the gut microbiome composition and metabolic functions and IR in children with obesity. In a cross-sectional study, fecal samples from children with obesity (10–16 years old) were collected for taxonomical and functional analysis of the fecal microbiome using shotgun metagenomics. The homeostatic model assessment for insulin resistance (HOMA-IR) was determined using fasting glucose and insulin. Associations between HOMA-IR and α-diversity measures as well as metabolic pathways were evaluated using Spearman correlations; relationships between HOMA-IR and β-diversity were assessed by permutational multivariate analysis of variance. Twenty-one children (nine males; median: age = 12.0 years; BMI z-score = 2.9; HOMA-IR = 3.6) completed the study. HOMA-IR was significantly associated with measures of α-diversity but not with β-diversity. Children with higher HOMA-IR exhibited lower overall species richness, Firmicutes species richness, and overall Proteobacteria species Shannon diversity. Furthermore, HOMA-IR was inversely correlated with the abundance of pathways related to the biosynthesis of lipopolysaccharides, amino acids, and short-chain fatty acids, whereas positive correlations between HOMA-IR and the peptidoglycan biosynthesis pathways were observed. In conclusion, insulin resistance was associated with decreased microbial α-diversity measures and abundance of genes related to the metabolic pathways. Our study provides a framework for understanding the microbial alterations in pediatric obesity.

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