scholarly journals Sow Vaccination Against Virulent Glaesserella Parasuis Shapes the Nasal Microbiota of Their Offspring

2022 ◽  
Author(s):  
Miguel Blanco-Fuertes ◽  
Florencia Correa-Fiz ◽  
Sergi Lopez-Serrano ◽  
Marina Sibila ◽  
Virginia Aragon
Keyword(s):  
Metabolic Pathways ◽  
Amplicon Sequencing ◽  
Microbiota Composition ◽  
Pork Industry ◽  
Virulent Strains ◽  
16S Amplicon Sequencing ◽  
Nasal Swabs ◽  
Group A ◽  
Distinctive Structure ◽  
Nasal Microbiota

Abstract Glaesserella parasuis is the etiological agent of Glässer’s disease, a common pathology in the pork industry with higher prevalence in the postweaning period. Vaccination is one of the strategies to control this disease. Here, we investigated the effect that sow vaccination against virulent strains of G. parasuis had in the nasal microbiota of their offspring. Nasal swabs from fifteen days-old piglets from vaccinated (vs-P, N=11) and unvaccinated sows (cs-P, N=11) were obtained and DNA was extracted for 16S amplicon sequencing. Microbiota composition was different, with lower diversity in vs-P, and a strong clustering of the groups in beta diversity analysis. Among the 1,509 sequences associated to either study group, all the sequences classified as G. parasuis (N=10) had lower relative abundance in the vs-P group. A list of 32 inferred metabolic pathways were statistically different between groups. A distinctive structure of the two microbial networks was detected, with modules in the cs-P not conserved in the vs-P network. In conclusion, vaccination of the sows had a large effect in the microbiota composition of their offspring that went beyond the effect on the targeted pathogen. The mechanisms underneath these changes may include alteration of the microbiota network due to the elimination of the targeted pathogen and/or immunological changes.

scholarly journals Larval Diet Abundance Influences Size and Composition of the Midgut Microbiota of Aedes aegypti Mosquitoes

2021 ◽  
Vol 12 ◽  
Author(s):  
Hannah J. MacLeod ◽  
George Dimopoulos ◽  
Sarah M. Short
Keyword(s):  
Aedes Aegypti ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Larval Diet ◽  
Microbiota Composition ◽  
Vector Species ◽  
Larval Food ◽  
Disease Vector ◽  
16S Amplicon Sequencing ◽  
The Impact

The midgut microbiota of the yellow fever mosquito Aedes aegypti impacts pathogen susceptibility and transmission by this important vector species. However, factors influencing the composition and size of the microbiome in mosquitoes are poorly understood. We investigated the impact of larval diet abundance during development on the composition and size of the larval and adult microbiota by rearing Aedes aegypti under four larval food regimens, ranging from nutrient deprivation to nutrient excess. We assessed the persistent impacts of larval diet availability on the microbiota of the larval breeding water, larval mosquitoes, and adult mosquitoes under sugar and blood fed conditions using qPCR and high-throughput 16S amplicon sequencing to determine bacterial load and microbiota composition. Bacterial loads in breeding water increased with increasing larval diet. Larvae reared with the lowest diet abundance had significantly fewer bacteria than larvae from two higher diet treatments, but not from the highest diet abundance. Adults from the lowest diet abundance treatment had significantly fewer bacteria in their midguts compared to all higher diet abundance treatments. Larval diet amount also had a significant impact on microbiota composition, primarily within larval breeding water and larvae. Increasing diet correlated with increased relative levels of Enterobacteriaceae and Flavobacteriaceae and decreased relative levels of Sphingomonadaceae. Multiple individual OTUs were significantly impacted by diet including one mapping to the genus Cedecea, which increased with higher diet amounts. This was consistent across all sample types, including sugar fed and blood fed adults. Taken together, these data suggest that availability of diet during development can cause lasting shifts in the size and composition of the microbiota in the disease vector Aedes aegypti.

Changes in the gut microbiota of morbidly obese patients after laparoscopic sleeve gastrectomy

2021 ◽  
Author(s):  
Alev Kural ◽  
Imran Khan ◽  
Hakan Seyit ◽  
Tuba R Caglar ◽  
Pınar Toklu ◽  
...  
Keyword(s):  
Sleeve Gastrectomy ◽  
Gut Microbiota ◽  
Laparoscopic Sleeve Gastrectomy ◽  
Amplicon Sequencing ◽  
Morbidly Obese ◽  
Microbiota Composition ◽  
16S Amplicon Sequencing ◽  
Before And After ◽  
Stool Samples ◽  
Gut Microbiota Composition

Aims: Permanent treatment of morbid obesity with medication or diet is nearly impossible. Laparoscopic sleeve gastrectomy (LSG) is becoming a widely accepted treatment option. This study profiled and compared gut microbiota composition before and after LSG. Methods & results: A total of 54 stool samples were collected from 27 morbidly obese individuals before and after LSG. The gut microbiota was profiled with 16S amplicon sequencing. After LSG, patients demonstrated a significant decrease (p < 0.001) in BMI and an increase in bacterial diversity. An increased Firmicutes/Bacteroidetes ratio was also noticed after LSG. The families Prevotellaceae and Veillonellaceae predominated in preoperative samples but were markedly lowered after LSG. A marked increase in Akkermansia, Alistipes, Streptococcus, Ruminococcus and Parabacteroides was observed after LSG. Conclusion: In addition to lowering BMI, LSG remodeled gut microbiota composition.

Correlation of gut microbial compositions to the development of Kawasaki disease vasculitis in children

2020 ◽  
Vol 15 (8) ◽  
pp. 591-600 ◽  
Author(s):  
Imran Khan ◽  
Xiao-ang Li ◽  
Betty Law ◽  
Ka In U ◽  
Bao Quan Pan ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
Gut Microbiota ◽  
Bacterial Pathogens ◽  
Amplicon Sequencing ◽  
Unknown Etiology ◽  
Fecal Dna ◽  
Microbiota Composition ◽  
Beneficial Bacteria ◽  
16S Amplicon Sequencing ◽  
Gut Microbiota Composition

Aim: Here, we hypothesize that dysbiotic gut microbiota might contribute to the development of Kawasaki disease (KD), a pediatric disease with unknown etiology. This is the second report on gut microbiota composition in KD patients. Materials & results: 16S amplicon sequencing was performed on fecal DNA samples and revealed predominance of bacterial pathogens, such as Fusobacterium, Neisseria, Shigella and Streptococcus, in the gut of KD patients, but absent or suppressed after immunoglobulin/antibiotics therapy. In addition, beneficial bacteria propagated after the therapy. Conclusion: We conclude that prevalence of Fusobacteria, Shigella and Streptococcus might contribute to KD pathogenesis.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Wenzhi Cui ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Large Scale ◽  
Low Cost ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Training Sample ◽  
Rrna Gene ◽  
16S Amplicon Sequencing ◽  
Cross Platform ◽  
Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

scholarly journals Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Hui ◽  
Paulina Tamez-Hidalgo ◽  
Tomasz Cieplak ◽  
Gizaw Dabessa Satessa ◽  
Witold Kot ◽  
...  
Keyword(s):  
Immune Modulation ◽  
Amplicon Sequencing ◽  
Saccharina Latissima ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Colon Mucosa ◽  
Weaned Piglets ◽  
Brown Macroalgae ◽  
Blood Concentrations ◽  
Significant Difference

Abstract Background The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. Results This study investigated the effect of using rapeseed-seaweed blend (rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima) fermented by lactobacilli (FRS) as feed ingredients in piglet weaning. From d 28 of life to d 85, the piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. In this period, no significant difference of piglet performance was found among the three groups. From a subset of piglets (n = 10 from each treatment), blood samples for hematology, biochemistry and immunoglobulin analysis, colon digesta for microbiome analysis, and jejunum and colon tissues for histopathological analyses were collected. The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier relative to the 0% FRS group. The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistency between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity. Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed, and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG. Conclusions FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets, improved the colon mucosa barrier with altered microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.

scholarly journals Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0241529
Author(s):  
Anita Silver ◽  
Sean Perez ◽  
Melanie Gee ◽  
Bethany Xu ◽  
Shreeya Garg ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Ground Beetle ◽  
Amplicon Sequencing ◽  
Carabid Beetles ◽  
Secretory Cells ◽  
Pygidial Gland ◽  
Defensive Compounds ◽  
Highly Active ◽  
16S Amplicon Sequencing ◽  
Host Diet

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types—guts, and pygidial gland secretory cells (which produce defensive compounds)—were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.

scholarly journals Dynamic alteration in the gut microbiota and metabolome during the pregnancy

2021 ◽  
Author(s):  
Peifeng Xie ◽  
Chengjun Hu ◽  
Qinghua He ◽  
Qian Zhu ◽  
Xiangfeng Kong
Keyword(s):  
Gut Microbiota ◽  
Metabolic Pathways ◽  
Late Pregnancy ◽  
Metabolite Profile ◽  
Microbiota Composition ◽  
Glutamate Metabolism ◽  
Fat Percentage ◽  
Rrna Sequencing ◽  
Dynamic Alteration ◽  
Gut Microbiota Composition

Abstract Background Gut microbiota and their metabolites were associated with obesity. Our previous study showed that maternal body fat percentage increased from days 45 to 110 of gestation in a Huanjiang mini-pig model. Thus, 16S rRNA sequencing and metabonomic techniques were used to investigate the changes of maternal gut microbiota composition and microbial metabolite profile from days 45 to 110 of gestation. Results The abundances of Clostridium_sensu_stricto_1, Romboutsia, Turicibacter, and Streptococcus in jejunum contents were higher in day 110 than those in day 45 or 75 of gestation. In ileum, the abundance of Streptococcus was the highest (P < 0.05) at day 110 of gestation, as well as the metabolism function of jejunal and ileal microbiota. The ileal butyrate and acetate concentrations were the highest at day 45 and day 110 of gestation, respectively. In colon, the concentrations of cadaverine and spermine were the highest (P < 0.05) at days 45 and 110 of gestation, respectively. Metabonomic analysis demonstrated that metabolic pathways including glutamine and glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and alanine, aspartate, and glutamate metabolism changed during gestation. Conclusions Microbiota composition and metabolites changed dramatically from the early to the late pregnancy, which might be associated with the maternal fat accumulation.

scholarly journals Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection

2020 ◽  
Author(s):  
Alex Grier ◽  
Ann L Gill ◽  
Haeja A Kessler ◽  
Anthony Corbett ◽  
Sanjukta Bandyopadhyay ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Disease ◽  
Disease Severity ◽  
Temporal Dynamics ◽  
Disease Risk ◽  
Developmental Trajectory ◽  
Microbiota Composition ◽  
Rsv Infection ◽  
Syncytial Virus ◽  
Nasal Microbiota

Abstract Rationale Respiratory Syncytial Virus (RSV) is a leading cause of infant respiratory disease. Infant airway microbiota has been associated with respiratory disease risk and severity. The extent to which interactions between RSV and microbiota occur in the airway, and their impact on respiratory disease susceptibility and severity, are unknown. Objectives Characterize temporal associations between microbiota and RSV infection before, during, and after infants’ first respiratory illness. Methods 16S rRNA microbiota profiling of two infant cohorts in the first year of life: 1) a cross-sectional cohort of 89 RSV infected infants sampled during illness and 102 matched healthy controls, and 2) a matched longitudinal cohort of 12 infants who developed RSV infection and 12 who did not, sampled before, during, and after infection. Results We identified 12 taxa significantly associated with RSV infection. All 12 taxa were differentially abundant during infection, with 8 associated with disease severity. Nasal microbiota composition was more discriminative of healthy vs. infected than of disease severity. Conclusions Our findings elucidate the chronology of nasal microbiota dysbiosis and suggest an altered developmental trajectory associated with RSV infection. Microbial temporal dynamics reveal indicators of disease risk, correlates of illness and severity, and impact of RSV infection on microbiota composition.

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