scholarly journals Nasopharyngeal microbiome composition associated with Streptococcus pneumoniae colonization suggests a protective role of Corynebacterium in young children

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257207
Author(s):  
Lei Xu ◽  
Joshua Earl ◽  
Michael E. Pichichero
Keyword(s):  
Streptococcus Pneumoniae ◽  
16S Rrna Gene Sequencing ◽  
Protective Role ◽  
Study Cohort ◽  
Rrna Gene ◽  
Upper Respiratory Infection ◽  
Microbiome Composition ◽  
Rrna Gene Sequencing

Streptococcus pneumoniae (Spn) is a leading respiratory tract pathogen that colonizes the nasopharynx (NP) through adhesion to epithelial cells and immune evasion. Spn actively interacts with other microbiota in NP but the nature of these interactions are incompletely understood. Using 16S rRNA gene sequencing, we analyzed the microbiota composition in the NP of children with or without Spn colonization. 96 children were included in the study cohort. 74 NP samples were analyzed when children were 6 months old and 85 NP samples were analyzed when children were 12 months old. We found several genera that correlated negatively or positively with Spn colonization, and some of these correlations appeared to be influenced by daycare attendance or other confounding factors such as upper respiratory infection (URI) or Moraxella colonization. Among these genera, Corynebacterium showed a consistent inverse relationship with Spn colonization with little influence by daycare attendance or other factors. We isolated Corynebacterium propinquum and C. pseudodiphtheriticum and found that both inhibited the growth of Spn serotype 22F strain in vitro.

scholarly journals Findings from the microbiota of tooth apical periodontitis and the search for pathogen forgranulomatous inflammation

2021 ◽  
Author(s):  
Yuanyuan Wang ◽  
Hao Xu ◽  
Minghui Wei ◽  
Yuhong Wang ◽  
Wenzhe Wang ◽  
...  
Keyword(s):  
Granulomatous Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Apical Periodontitis ◽  
Rrna Gene ◽  
Normal Microbiota ◽  
Rrna Gene Sequencing ◽  
Neisseria Subflava ◽  
Foot Pad

Abstract BackgroundOrofacial granulomatosis (OFG) is a granulomatous inflammation (GI) disease in maxillofacial region, the underlying cause of it remains unknown. Our previous study demonstrated that tooth apical periodontitis (AP) plays a significant role in the pathogenesis of OFG, we aimed here to characterize the AP bacterial signatures of OFG patients, and identify bacteria that may be important pathogens capable of inducing OFG.ResultsThe composition of AP microbiota in OFG cases and common AP controls was compared using 16S rRNA gene sequencing, the results showed a specific AP microbiota signature in OFG patients, characterized by domination of phyla Firmicutes and Proteobacteria , notably members of Streptococcus, Lactobacillus and Neisseria. To assess the pathogenicity of the potential pathogens in OFG, we isolated and successfully in vitro cultured Streptococcus, Lactobacillus casei, Neisseria subflava, Veillonella parvula and Actinomyces from OFG patients, and injected the clinical isolates into mice respectively. Ultimately, foot pad injection with N. subflava elicited granulomatous inflammation, and the virulence of N. subflava was verified based on Koch’s postulates.ConclusionsOur findings confirmed the role of bacteria in OFG, and first suggested that the component of the host normal microbiota, N. subflava is likely a pathogen for GI.

scholarly journals The growth response of rice (Oryza sativa L. var. FARO 44) in vitro after inoculation with bacterial isolates from a typical ferruginous ultisol

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Musa Saheed Ibrahim ◽  
Beckley Ikhajiagbe
Keyword(s):  
16S Rrna ◽  
Bacillus Cereus ◽  
Proteus Mirabilis ◽  
Growth Response ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rice Seedlings ◽  
Rrna Gene Sequencing

Abstract Background Rice forms a significant portion of food consumed in most household worldwide. Rice production has been hampered by soil factors such as ferruginousity which has limited phosphorus availability; an important mineral component for the growth and yield of rice. The presence of phosphate-solubilizing bacteria (PSB) in soils has been reported to enhance phosphate availability. In view of this, the present study employed three bacteria species (BCAC2, EMBF2 and BCAF1) that were previously isolated and proved P solubilization capacities as inocula to investigate the growth response of rice germinants in an in vitro setup. The bacteria isolates were first identified using 16S rRNA gene sequencing and then applied as inoculum. The inolula were prepared in three concentrations (10, 7.5 and 5.0 ml) following McFarland standard. Viable rice (var. FARO 44) seeds were sown in petri dishes and then inoculated with the three inocula at the different concentrations. The setup was studied for 28 days. Results 16S rRNA gene sequencing identified the isolates as: isolate BCAC2= Bacillus cereus strain GGBSU-1, isolate BCAF1= Proteus mirabilis strain TL14-1 and isolate EMBF2= Klebsiella variicola strain AUH-KAM-9. Significant improvement in rice germination, morphology, physiology and biomass parameters in the bacteria-inoculated setups was observed compared to the control. Germination percentage after 4 days was 100 % in the inoculated rice germinants compared to 65% in the control (NiS). Similarly, inoculation with the test isolates enhanced water-use efficiency by over 40%. The rice seedlings inoculated with Bacillus cereus strain GGBSU-1 (BiS) showed no signs of chlorosis and necrosis throughout the study period as against those inoculated with Proteus mirabilis strain TL14-1 (PiS) and Klebsiella variicola strain AUH-KAM-9 (KiS). Significant increase in chlorophyll-a, chlorophyll-b and alpha amylase was observed in the rice seedlings inoculated with BiS as against the NiS. Conclusion Inoculating rice seeds with Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 in an in vitro media significantly improved growth parameters of the test plant. Bacillus cereus strain GGBSU-1 showed higher efficiency due to a more improved growth properties observed.

scholarly journals Gut microbiota accelerates cisplatin-induced acute liver injury associated with robust inflammation and oxidative stress in mice

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Shenhai Gong ◽  
Yinglin Feng ◽  
Yunong Zeng ◽  
Huanrui Zhang ◽  
Meiping Pan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Metabolomic Analysis ◽  
Rrna Gene Sequencing ◽  
And Oxidative Stress

Abstract Background Gut microbiota has been reported to be disrupted by cisplatin, as well as to modulate chemotherapy toxicity. However, the precise role of intestinal microbiota in the pathogenesis of cisplatin hepatotoxicity remains unknown. Methods We compared the composition and function of gut microbiota between mice treated with and without cisplatin using 16S rRNA gene sequencing and via metabolomic analysis. For understanding the causative relationship between gut dysbiosis and cisplatin hepatotoxicity, antibiotics were administered to deplete gut microbiota and faecal microbiota transplantation (FMT) was performed before cisplatin treatment. Results 16S rRNA gene sequencing and metabolomic analysis showed that cisplatin administration caused gut microbiota dysbiosis in mice. Gut microbiota ablation by antibiotic exposure protected against the hepatotoxicity induced by cisplatin. Interestingly, mice treated with antibiotics dampened the mitogen-activated protein kinase pathway activation and promoted nuclear factor erythroid 2-related factor 2 nuclear translocation, resulting in decreased levels of both inflammation and oxidative stress in the liver. FMT also confirmed the role of microbiota in individual susceptibility to cisplatin-induced hepatotoxicity. Conclusions This study elucidated the mechanism by which gut microbiota mediates cisplatin hepatotoxicity through enhanced inflammatory response and oxidative stress. This knowledge may help develop novel therapeutic approaches that involve targeting the composition and metabolites of microbiota.

scholarly journals Live Bacillus subtilis natto Promotes Rumen Fermentation by Modulating Rumen Microbiota In Vitro

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1519
Author(s):  
Meinan Chang ◽  
Fengtao Ma ◽  
Jingya Wei ◽  
Junhao Liu ◽  
Xuemei Nan ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
Rumen Fluid ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rumen Fermentation ◽  
Rrna Gene ◽  
Bacillus Subtilis Natto ◽  
Rrna Gene Sequencing

Previous studies have shown that Bacillus subtilis natto affects rumen fermentation and rumen microbial community structure, which are limited to detect a few microbial abundances using traditional methods. However, the regulation of B. subtilis natto on rumen microorganisms and the mechanisms of microbiota that affect rumen fermentation is still unclear. This study explored the effects of live and autoclaved B. subtilis natto on ruminal microbial composition and diversity in vitro using 16S rRNA gene sequencing and the underlying mechanisms. Rumen fluid was collected, allocated to thirty-six bottles, and divided into three treatments: CTR, blank control group without B. subtilis natto; LBS, CTR with 109 cfu of live B. subtilis natto; and ABS, CTR with 109 cfu of autoclaved B. subtilis natto. The rumen fluid was collected after 0, 6, 12, and 24 h of fermentation, and pH, ammonia nitrogen (NH3-N), microbial protein (MCP), and volatile fatty acids (VFAs) were determined. The diversity and composition of rumen microbiota were assessed by 16S rRNA gene sequencing. The results revealed LBS affected the concentrations of NH3-N, MCP, and VFAs (p < 0.05), especially after 12 h, which might be attributed to changes in 18 genera. Whereas ABS only enhanced pH and NH3-N concentration compared with the CTR group (p < 0.05), which might be associated with changes in six genera. Supplementation with live B. subtilis natto improved ruminal NH3-N and propionate concentrations, indicating that live bacteria were better than autoclaved ones. This study advances our understanding of B. subtilis natto in promoting ruminal fermentation, providing a new perspective for the precise utilization of B. subtilis natto in dairy rations.

scholarly journals Assessing the contribution of biofilm to bacterial growth during stagnation in shower hoses

2020 ◽  
Vol 20 (7) ◽  
pp. 2564-2576
Author(s):  
Hongxi Peng ◽  
Ya Zhang ◽  
Ruowei Wang ◽  
Jingqing Liu ◽  
Wen-Tso Liu
Keyword(s):  
Water Quality ◽  
Fresh Water ◽  
Bacterial Growth ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Water Usage ◽  
Water Supplies ◽  
Biological Water ◽  
Rrna Gene Sequencing

Abstract Stagnation occurs in building water supplies when there is little or no water usage. As a result, the number of bacteria increase, and this often leads to the deterioration of water quality. Still, the role of biofilm in stagnation remains unclear. This study used shower hoses as the model system and investigated the contribution of biofilm and microbes in fresh water to the bacterial growth in water under different stagnation times from 6 to 24 h. Bacterial counts in water were observed to increase significantly after 12 h stagnation but longer stagnation did not lead to further increase, indicating different mechanisms contributing to bacterial growth during stagnation. 16S rRNA gene sequencing and Sourcetracker2 further confirmed that the contribution of fresh water to the microbial core community did not increase significantly with stagnation time, whereas the contribution of biofilm increased significantly after 24 h stagnation (53.5%) compared with 6 h stagnation (11.2%) (p &lt; 0.05). The present results differentiated the contribution between planktonic and biofilm phase to the bacterial growth during stagnation, and provided insights into its mechanism. These findings serve as a framework for future development of strategies to manage biological water quality at the distal end of the building water supplies.

scholarly journals Personalized Bioconversion of Panax Notoginseng Saponins Mediated by Gut Microbiota Between Chinese-diet and Western-diet Healthy Subjects

2021 ◽  
Author(s):  
Li Wang ◽  
Man-Yun Chen ◽  
Li Shao ◽  
Wei Zhang ◽  
Xiang-Ping Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Lactobacillus Rhamnosus ◽  
16S Rrna Gene Sequencing ◽  
Panax Notoginseng ◽  
Rrna Gene ◽  
Bifidobacterium Adolescentis ◽  
Correlative Analysis ◽  
Rrna Gene Sequencing ◽  
The Relationship

Abstract Background: Panax notoginseng saponins (PNS) as the main effective substances from P. notoginseng with low bioavailability could be bio-converted by human gut microbiota. In our previous study, PNS metabolic variations mediated by gut microbiota have been observed between high fat, high protein (HF-HP)-diet and low fat, plant fiber-rich (LF-PF)-diet subjects. In this study, we aimed to correspondingly characterize the relationship between distinct gut microbiota profiles and PNS metabolites. Methods: Gut microbiota were collected from HF-HP and LF-PF healthy adults, respectively and profiled by 16S rRNA gene sequencing. PNS were incubated with gut microbiota in vitro. A LC-MS/MS method was developed to quantify the five main metabolites yields including ginsenoside F1 (GF1), ginsenoside Rh2 (GRh2), ginsenoside compound K (GC-K), protopanaxatriol (PPT) and protopanaxadiol (PPD). The selected microbial species, Bifidobacterium adolescentis and Lactobacillus rhamnosus, were employed to metabolize PNS for the corresponding metabolites.Results: The five main metabolites were significantly different between the two diet groups. Compared with HF-HP group, the microbial genus Blautia, Bifidobacterium, Clostridium, Corynebacterium, Dorea, Enhydrobacter, Lactobacillus, Roseburia, Ruminococcus, SMB53, Streptococcus, Treponema and Weissella were enriched in LF-PF group, while Phascolarctobacterium and Oscillospira were relatively decreased. Furthermore, Spearman’s correlative analysis revealed gut microbiota enriched in LF-PF and HF-HP groups were positively and negatively associated with PNS metabolites yields, respectively. Conclusions: Our data showed gut microbiota diversity led to the personalized bioconversion of PNS.

scholarly journals Analysis of Vaginal and Endometrial Microbiota Communities in Infertile Women With a History of Repeated Implantation Failure

2020 ◽  
Author(s):  
Takuhiko Ichiyama ◽  
Keiji Kuroda ◽  
Yoko Nagai ◽  
Daichi Urushiyama ◽  
Motoharu Ono ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Implantation Failure ◽  
Repeated Implantation Failure ◽  
Infertile Women ◽  
Healthy Women ◽  
History Of ◽  
Rrna Gene Sequencing ◽  
Clinical Trials Registry

Abstract Background: Repeated implantation failure (RIF) is estimated to occur in 15%–20% of infertile women undergoing in vitro fertilization-embryo transfer (IVF-ET). Molecular identification recently confirmed that the uterine microbiota may have implications for reproductive and obstetrical outcomes. One hundred forty-five women who had been diagnosed with RIF were enrolled in the study. Twenty-one healthy women were also enrolled as controls. We investigated their vaginal and endometrial microbiotas using 16S rRNA gene sequencing and compared the microbiota profiles in the patients with RIF and controls.Results: The endometrial microbiotas had higher α-diversities than did the vaginal microbiotas (p<0.001 in both patients with RIF and healthy women). The microbiota profiles showed that vaginal and endometrial samples in patients with RIF had significantly higher levels of 5 and 14 bacterial genera, respectively, than those in healthy women. These genera included Atopobium, Gardnerella, Prevotella and Megasphaera. Vaginal Lactobacillus rates in patients with RIF were significantly lower at 76.4 ± 38.9% compared with those of the controls at 91.8 ± 22.7% (p=0.018), but endometrial Lactobacillus rates did not significantly differ between the RIF patients and controls (56.2 ± 36.4% and 58.8 ± 37.0%, respectively, p=0.79) Conclusions: Impaired microbiota communities containing specific bacteria in both the endometrium and vagina were associated with implantation failure. The Lactobacillus rate in the vagina, but not the endometrium, may be a biomarker for RIF.Trial registration: UMIN Clinical Trials Registry, UMIN000031731, Registered 15 March 2018; https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000036121

scholarly journals Dietary sphinganine is selectively assimilated by members of the gut microbiome

2020 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H. Le ◽  
Elizabeth L. Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Bioactive Components ◽  
Microbiome Composition ◽  
Metabolic Products ◽  
Comparative Metabolomics ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

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