Ribosomal Ribonucleic Acid Gene Sequencing Research Articles

Effects of Pretreatment with Bifidobacterium bifidum Using 16S Ribosomal RNA Gene Sequencing in a Mouse Model of Acute Colitis Induced by Dextran Sulfate Sodium.

BackgroundBifidobacterium is a potentially effective and safe treatment for patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease. However, information on the influence of B. bifidum on gut microbial diversity of treated and pretreated IBD patients is limited.Material/MethodsOur study investigated therapeutic and preventive effects of B. bifidum ATCC 29521 on C57BL/6 mice with dextran sulfate sodium (DSS)-induced acute colitis via 16S ribosomal ribonucleic acid (rRNA) gene sequencing.ResultsTreatment and pretreatment of mice with B. bifidum ATCC 29521 significantly alleviated the severity of acute colitis on the basis of clinical and pathologic indicators. 16S rRNA gene sequencing showed that administration of B. bifidum shifted composition of the gut microbiome in mice with DSS-induced colitis in both treated and pretreated groups. Mice pretreated with B. bifidum ATCC 29521 for 21 days exhibited a significant increase in diversity of the gut microbiome. Principal coordinate analysis showed that gut microbiota structure was shaped by different treatments and time points. On the basis of linear discriminant analysis of effect size, the abundance of the genus Escherichia-Shigella, belonging to the family Enterobacteriaceae, was reduced in the B. bifidum-treated group, indicating that pathogens were inhibited by the B. bifidum treatment. Furthermore, the genera Intestinimonas and Bacteroides were significantly associated with the B. bifidum-pretreated group.Conclusions16S rRNA gene sequencing showed that pretreatment with B. bifidum ATCC 29521 reduced intestinal inflammation and altered the gut microbiota to favor the genera Intestinimonas and Bacteroides.

Oral microbiome and pancreatic cancer.

BACKGROUNDMicrobiota profiles differ between patients with pancreatic cancer and healthy people, and understanding these differences may help in early detection of pancreatic cancer. Saliva sampling is an easy and cost-effective way to determine microbiota profiles compared to fecal and tissue sample collection.AIMTo investigate the saliva microbiome distribution in patients with pancreatic adenocarcinoma (PDAC) and the role of oral microbiota profiles in detection and risk prediction of pancreatic cancer.METHODSWe conducted a prospective study of patients with pancreatic cancer (n = 41) and healthy individuals (n = 69). Bacterial taxa were identified by 16S ribosomal ribonucleic acid gene sequencing, and a linear discriminant analysis effect size algorithm was used to identify differences in taxa. Operational taxonomic unit values of all selected taxa were converted into a normalized Z-score, and logistic regressions were used to calculate risk prediction of pancreatic cancer.RESULTSCompared with the healthy control group, carriage of Streptococcus and Leptotrichina (z-score) was associated with a higher risk of PDAC [odds ratio (OR) = 5.344, 95% confidence interval (CI): 1.282-22.282, P = 0.021 and OR = 6.886, 95%CI: 1.423-33.337, P = 0.016, respectively]. Veillonella and Neisseria (z-score) were considered a protective microbe that decreased the risk of PDAC (OR = 0.187, 95%CI: 0.055-0.631, P = 0.007 and OR = 0.309, 95%CI: 0.100-0.952, P = 0.041, respectively). Among the patients with PDAC, patients reporting bloating have a higher abundance of Porphyromonas (P = 0.039), Fusobacterium (P = 0.024), and Alloprevotella (P = 0.041); while patients reporting jaundice had a higher amount of Prevotella (P = 0.008); patients reporting dark brown urine had a higher amount of Veillonella (P = 0.035). Patients reporting diarrhea had a lower amount of Neisseria and Campylobacter (P = 0.024 and P = 0.034), and patients reporting vomiting had decreased Alloprevotella (P = 0.036).CONCLUSIONSaliva microbiome was able to distinguish patients with pancreatic cancer and healthy individuals. Leptotrichia may be specific for patients living in Sichuan Province, southwest China. Symptomatic patients had different bacteria profiles than asymptomatic patients. Combined symptom and microbiome evaluation may help in the early detection of pancreatic cancer.

Ocular Surface Microbiome in Health and Disease.

The ocular surface is exposed continuously to the environment and, as a consequence, to a variety of different microbes. After the results of the Human Microbiome Project became publicly available, international research groups started to focus interest on exploring the ocular surface microbiome and its physiopathological relationship to the eye. For example, numerous research studies the existence of the ocular surface's bacterial flora, typically gathering cultures from healthy patients and finding few variations in the bacterial species. More recently, culture-independent methods, including 16S ribosomal ribonucleic acid (rRNA) gene sequencing, are being used to define the ocular microbiome. These newer methods suggest that the microbial communities have a greater diversity than previously reported. These communities seem to serve an immune-modulating function and maintain relationships with other microbes and organs, even distant ones. This review summarizes the literature exploring the ocular microbiome, both in health and in different diseases.

Newly introduced Cardinium endosymbiont reduces microbial diversity in the rice brown planthopper Nilaparvata lugens.

Symbiotic microorganisms in invertebrates play vital roles in host ecology and evolution. Cardinium, a common intracellular symbiont, is transinfected into the important agricultural pest Nilaparvata lugens (rice brown planthopper) to regulate its reproduction, but how this impacts its microbial community is unknown. Here, we characterized the bacterial microbiota from N. lugens, with or without Cardinium, at different developmental stages and in various adult tissues using 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing. Upon infection with Cardinium, we found that microbial diversity in the different developmental stages of N. lugens (especially females), and in female midguts and male testes, was lower than that in the uninfected control. There was a negative correlation between Cardinium and most related genera and between Bacteroidetes and Proteobacteria. Although the microbial structure varied during Cardinium infection, Acinetobacter spp. were a core microbiome genus. The Cardinium infection enhanced the relative density of midgut-associated Acinetobacter spp., with both bacteria exhibiting tissue-specific tropism. In addition, this infection caused the changes of main microbial functions in N. lugens. These results offer insights into the effects of alien (i.e. newly introduced from other organism) Cardinium infection on N. lugens-associated microbiotas, aiding in the development of transinfected endosymbionts for pest control.

The relationship between the rumen microbiome and carcass merit in Angus steers.

The objective of this study was to explore the relationships between ruminal microbial populations from Angus steers that were divergent in carcass traits related to adipose accumulation. Twenty-four feedlot-finished Angus steers (age: 538 ± 21 d; body weight following lairage: 593.9 ± 43.7 kg) were slaughtered, and ruminal contents and carcass data were collected. Ruminal microbial deoxyribonucleic acid (DNA) extraction and 16S ribosomal ribonucleic acid (rRNA) gene sequencing were performed to determine microbial relative abundances, to estimate microbial diversity, and to predict microbial metabolic pathways. A variety of correlation analyses and one-way ANOVA were performed to investigate the relationships between the rumen microbiome and carcass traits. Marbling score (P = 0.001) and longissimus lipid content (P = 0.009) were positively correlated to Chao1 Richness Index, suggesting that increased intramuscular fat was associated with increased numbers of ruminal microbial species. The phyla Tenericutes and TM7 were negatively correlated (P ≤ 0.05) to marbling score and longissimus lipid content, indicating that lower abundances of these phyla may be associated with improvements in intramuscular fat content. Greater abundance of the bacterial family S24-7 was positively correlated (P = 0.002) to marbling score. Analysis by marbling classification revealed further linkages to microbial richness (P ≤ 0.063), diversity (P = 0.044), and S24-7 (P < 0.001) populations. Computational prediction of the microbial metabolic pathways revealed no differences (P ≥ 0.05) in metabolic pathway expression in rumen microbes between steers in the high- and low-marbling classes. Several phyla, families, and genera were positively correlated (P ≤ 0.05) to both rib fat thickness and yield grade. Collectively, our results suggest that microbial composition is associated to differing performance in carcass adipose traits. Overall, most of the bacterial taxa correlated to the intramuscular and subcutaneous fat depots did not overlap, suggesting the microbial population end products likely impacted adipose accumulation largely via separate adipogenic pathways of the host animal.

THMs, HAAs and NAs production from culturable microorganisms in pipeline network by ozonation, chlorination, chloramination and joint disinfection strategies

Disinfection is an indispensable process to inactivate pathogens, while unexpected disinfection by-products (DBPs) would also be formed between the reaction of residual disinfectants and microorganisms in the water distribution system (WDS). However, there are few studies referring to the formation of DBPs and DBPs-associated toxicity under various disinfection methods based on microorganisms in the real WDS. In addition, the main contributors of bacterial communities or components that generate DBPs are unclear. In this study, the formation of trihalomethanes (THMs), halo-acetic acids (HAAs), nitrosamines (NAs) from culturable microorganisms in pipeline network by ozonation(O3), chlorination (Cl2), chloramination (NH2Cl) and joint disinfection methods were compared, meanwhile, their calculated toxicities under different oxidation scenarios were also discussed. Moreover, 16S ribosomal ribonucleic acid (rRNA) gene sequencing was used to identify the main microbial communities. The results demonstrated that THMs and HAAs increased with increasing disinfectant dosages, while the quantity of NAs (mainly nitroso dimethylamine (NDMA)) was not significantly related to disinfectant dosages for each disinfection strategy. Chloroform (TCM) and dichloroacetic acid (DCAA) were the dominant THMs and HAAs species, respectively. NDMA existed in the samples before disinfections, which may due to the metabolic activity of microorganisms. Pre-O3 increased THMs formation during subsequent Cl2 and NH2Cl treatment. However, pre-O3 effectively reduced HAAs produced by subsequent chlorination. O3/Cl2 disinfection had the highest DBPs formation potential (DBPFP) (883.6 nM), while its calculated toxicity was similar to that in Cl2 disinfection treatment. Pseudomonas was the most abundant bacterial genus in biofilm of WDS pipeline. This study can aid in an optimal disinfection strategy for water treatment plants to reduce the toxicity of DBPs caused by biomass in pipelines and ensure water quality safety.

The microbiome of pediatric patients with chronic rhinosinusitis.

This study aimed to compare the microbiota of pediatric patients with chronic rhinosinusitis (CRS) who are undergoing adenoidectomy to treat their disease with that of healthy control patients. Patients undergoing adenoidectomy-only for obstructive sleep apnea (n = 50) and CRS (n = 37) were recruited. Preoperative 22-item Sino-Nasal Outcome Test (SNOT-22) or Sinus and Nasal Quality of Life Survey (SN-5) were collected. Each patient had samples collected from their nasopharynx (adenoid bed) and nasal cavity (sinus) at the onset of surgery. 16S ribosomal ribonucleic acid (rRNA) gene sequencing was subsequently performed to obtain per sample taxonomic abundances. Statistical analyses included permutational multivariate analysis of variance (PERMANOVA), alpha (within sample) diversity measures, and changes in taxonomic abundance. Moraxella was the most abundant organism. Nasopharyngeal swabs demonstrated higher alpha diversity compared to the nasal cavity. The diversity was not different based on CRS vs obstructive history. There was an increase in diversity with increasing age, and eczema contributed to a greater difference in diversity between the nasopharynx and nasal cavity. Diversity was not affected by adenoid size; however, use of nasal steroids, inhaled steroids, and antihistamines influenced diversity in both the nasopharynx and nasal cavity. Nasopharyngeal samples were higher in relative abundance for Fusobacterium, Prevotella, Porphyromonas, and Campylobacter compared to the nasal cavity. The nasopharynx and nasal cavity differed in both microbiota composition and diversity. In contrast, no significant difference in composition or diversity were found in CRS vs control patients. Ecological changes in the nasopharyngeal and sinus site may contribute to the etiology for adenoid hypertrophy in both healthy controls and CRS patients.

Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

BackgroundCareful consideration of experimental artefacts is required in order to successfully apply high-throughput 16S ribosomal ribonucleic acid (rRNA) gene sequencing technology. Here we introduce experimental design, quality control and “denoising” approaches for sequencing low biomass specimens.ResultsWe found that bacterial biomass is a key driver of 16S rRNA gene sequencing profiles generated from bacterial mock communities and that the use of different deoxyribonucleic acid (DNA) extraction methods [DSP Virus/Pathogen Mini Kit® (Kit-QS) and ZymoBIOMICS DNA Miniprep Kit (Kit-ZB)] and storage buffers [PrimeStore® Molecular Transport medium (Primestore) and Skim-milk, Tryptone, Glucose and Glycerol (STGG)] further influence these profiles. Kit-QS better represented hard-to-lyse bacteria from bacterial mock communities compared to Kit-ZB. Primestore storage buffer yielded lower levels of background operational taxonomic units (OTUs) from low biomass bacterial mock community controls compared to STGG. In addition to bacterial mock community controls, we used technical repeats (nasopharyngeal and induced sputum processed in duplicate, triplicate or quadruplicate) to further evaluate the effect of specimen biomass and participant age at specimen collection on resultant sequencing profiles. We observed a positive correlation (r = 0.16) between specimen biomass and participant age at specimen collection: low biomass technical repeats (represented by < 500 16S rRNA gene copies/μl) were primarily collected at < 14 days of age. We found that low biomass technical repeats also produced higher alpha diversities (r = − 0.28); 16S rRNA gene profiles similar to no template controls (Primestore); and reduced sequencing reproducibility. Finally, we show that the use of statistical tools for in silico contaminant identification, as implemented through the decontam package in R, provides better representations of indigenous bacteria following decontamination.ConclusionsWe provide insight into experimental design, quality control steps and “denoising” approaches for 16S rRNA gene high-throughput sequencing of low biomass specimens. We highlight the need for careful assessment of DNA extraction methods and storage buffers; sequence quality and reproducibility; and in silico identification of contaminant profiles in order to avoid spurious results.

Isolation, Identification and Biotechnological Applications of a Novel, Robust, Free-living Chlorococcum (Oophila) amblystomatis Strain Isolated from a Local Pond

Bioprospection of novel autochthonous strains is key to the successful industrial-scale production of microalgal biomass. A novel Chlorococcum strain was recently isolated from a pond inside the industrial production facility of Allmicroalgae (Leiria, Portugal). Phylogenetic analysis based on 18S ribosomal ribonucleic acid (rRNA) gene sequences suggests that this isolate is a novel, free-living Oophila amblystomatis strain. However, as our phylogenetic data strongly suggests that the aforementioned taxon belongs to the genus Chlorococcum, it is here proposed to rename this species as Chlorococcum amblystomatis. In order to characterize the biotechnological potential of this novel isolate, growth performance and biochemical composition were evaluated from the pilot (2.5-m3) to industrial (10-m3) scale. The highest maximum areal productivity (36.56 g·m−2·day−1) was reached in a 10-m3 tubular photobioreactor (PBR), as compared to that obtained in a 2.5-m3 PBR (26.75 g·m−2·day−1). Chlorococcum amblystomatis displayed high protein content (48%–56% dry weight (DW)) and moderate levels of total lipids (18%–31% DW), carbohydrates (6%–18% DW) and ashes (9%–16% DW). Furthermore, the lipid profile was dominated by polyunsaturated fatty acids (PUFAs). The highest pigment contents were obtained in the 2.5-m3 PBR, where total chlorophylls accounted for 40.24 mg·g−1 DW, followed by lutein with 5.37 mg·g−1 DW. Overall, this free-living Chlorococcum amblystomatis strain shows great potential for nutritional applications, coupling a promising growth performance with a high protein content as well as relevant amounts of PUFAs, chlorophyll, and carotenoids.

Effect of time restricted feeding on the gut microbiome in adults with obesity: A pilot study.

Time restricted feeding is a form of intermittent fasting where participants shorten the daily window in which they eat. This is the first study to examine the effects of intermittent fasting on changes in the gut microbiome. Adults with obesity (n = 14) participated in a daily 8-hour time restricted feeding intervention (8-hour feeding window/16-hour fasting window) for 12 weeks. Fecal microbiota were determined by 16 S rRNA (ribosomal ribonucleic acid) gene sequencing of stool samples. Body weight decreased (P < 0.05) by -2 ± 1 kg. Gut microbiota phylogenetic diversity remained unchanged. The two most common phyla were Firmicutes and Bacteroidetes accounting for 61.2% and 26.9% of total abundance at baseline. No significant alterations in the abundance of Firmicutes, Bacteroidetes, or any other phyla were detected after 12 weeks of time restricted feeding. Time restricted feeding did not significantly alter the diversity or overall composition of the gut microbiome.

Spatial analysis of bacteria in brackish lake sediment

The spatial distribution of bacterial communities inhabiting sediment is heterogeneous at different spatial scales, but mostly unexplored. Here, it is postulated that the heterogeneity of the bacterial community composition varies at the same scale of the heterogeneity of sediment chemical properties. The large spatial scale (km) diversity in sediment from a brackish water lagoon (Chilika Lake, India) is studied, considering the large scale physical and chemical characteristics of land cover, climate, pH, and salinity. Seventy-two samples (24 stations, 3 seasons: winter, rainy, and summer) of sediment from Chilika Lake were analyzed by 16S ribosomal ribonucleic acid (rRNA) gene sequencing, and the relations with land cover and other physico-chemical parameters are discussed. More samples were collected after a severe cyclonic storm (Phailin) passed near the lagoon in 2013, to see the impact of the tropical storm on the spatial and temporal distribution of bacteria in the sediment. The results demonstrate clear spatial relations between physico-chemical parameters (e.g., salinity), land surfaces (e.g., drainage area), and the distribution of sediment microbial communities.

Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis.

BackgroundOral daily tenofovir (TFV) disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective for HIVprevention, yet long-term effects are not fully understood. We investigated the effects of PrEP on the rectal microbiome in a cohort of men who have sex with men (MSM).MethodsThis cross-sectional analysis included HIV-negative MSM either on PrEP (n = 37) or not (n = 37) selected from an ongoing cohort using propensity score matching. Rectal swabs were used to examine microbiome composition using 16S ribosomal ribonucleic acid gene sequencing, and associations between PrEP use and microbiota abundance were examined. Hair specimens were used to quantify TFV and FTC exposure over the past 6 weeks on a subset of participants (n = 15).ResultsPre-exposure prophylaxis use was associated with a significant increase in Streptococcus abundance (adjusted P = .015). Similar associations were identified using least absolute shrinkage and selection operator (LASSO) regression, confirming the increase in Streptococcus and also showing increased Mitsuokella, Fusobacterium, and decreased Escherichia/Shigella. Increased Fusobacterium was significantly associated with increasing TFV exposure.ConclusionsOral TDF/FTC for PrEP is associated with rectal microbiome changes compared to well matched controls, specifically increased Streptococcus and Fusobacterium abundance. This study highlights the need for future investigations of the role of microbiome changes on HIV susceptibility and effectiveness of PrEP.

Isolation and characterization of novel and efficient protease producing bacteria from drinking water resources

AbstractAn attempt has been made to explore the stability of protease enzyme (isolated from Bacillus sp.) by statistical method. More than 100 isolates were screened for extracellular protease activity derived from various potable water samples of Mahabubnagar district, Telangana State, India. The activity of protease is found to be varying from sample to sample, the highest being reported by the isolate from water sample of Kalwakurthy mandal, Mahabubnagar district and therefore was selected for further studies. The 16S rRNA (ribosomal ribonucleic acid) gene sequence of the isolate showed closest similarity with Bacillus sp. and the sequence was submitted to National Center for Biotechnology Information (NCBI) gene bank (accession number GU566359) and the culture was deposited in three international culture deposition centers (KCTC-13725: MTCC-10465: JCM-16713). The present study revealed that, this Bacillus sp. showed a greater amount of protease production with the inherent characters of thermo, alkali and oxidant stability which makes it a potential alternative protease producing strain in various industrial applications.

Occurrence of Cryptosporidium and Giardia in potable water sources in Chandigarh, Northern India

AbstractContamination with Cryptosporidium and Giardia from drinking water sources in a city in Northern India was assessed. A protocol modified from a standard ISO protocol, which includes filtration, concentration, separation and detection steps, was tested and showed comparable recovery efficiencies (Giardia mean = 77.4%, Cryptosporidium mean = 61.8% from the modified protocol, compared with Giardia mean = 61.6%, Cryptosporidium mean = 69% from the ISO protocol) at a substantial cost reduction. This protocol was used for analysing 71 samples of potable water from different areas of Chandigarh, where sampling locations were divided into groups according to the population density, which also partially equates with the level of infrastructure. Samples were collected during (n = 29) and outside the monsoon season (n = 42). Of all samples analysed, 16 (22.5%) were Cryptosporidium- and/or Giardia-positive. Parasites per sample were low (1–10 (oo)cysts per 10 L), although one sample contained large numbers of Giardia cysts (&gt;1,000). Polymerase chain reaction analyses on the small subunit ribosomal ribonucleic acid (SSU rRNA), triose-phosphate isomerase (tpi), glutamate dehydrogenase (gdh) and beta-giardin (bg) gene sequences on Giardia-positive samples and SSU rRNA on Cryptosporidium-positive samples tended to be unsuccessful, although Giardia cysts of Assemblages B and C were identified. No association with the season was detected, but an association with the location of water supply was identified. Samples from areas with the lowest infrastructure were not associated with higher levels of contamination, but samples from the middle level were significantly more likely to be contaminated than those from the highest level of infrastructure. Results indicate that even in a city with a well-developed infrastructure, the contamination of potable water with protozoan parasites remains a public health risk.

The biofilm in bacterial vaginosis: implications for epidemiology, diagnosis and treatment: 2018 update.

Bacterial vaginosis is conventionally appreciated as a temporary community disturbance of the vaginal microbiota, though really involving self-organization as a resilient biofilm community. We will briefly review here how recent findings on this matter may affect practice and research in this field. The rapidly expanding literature base on the vaginal microbiome is largely based on 16S ribosomal ribonucleic acid (rRNA) and cpn60 gene sequencing, with few studies accounting thus far for spatial microbiota organization. The putative sexually transmitted disease profile of bacterial vaginosis inferred from epidemiologic research, may concur with its biofilm nature, notably involving spread of dispersed cells or cell aggregates between hosts. De novo biofilm formation in response to prolonged vaginal ecosystem pressure should be considered a pathogenetic model as well. Biofilm assays may not only aid epidemiologic research, but also add to monitoring therapeutic efficacy of novel treatments. Therapeutic research thus far is largely confined to inhibition of in-vitro biofilm formation, though a recent innovative clinical trial involved a combinational approach of metronidazole and a surfactant, specifically aiming for the biofilm. Bacterial vaginosis research will further benefit from biofilm assays complementing taxonomy-based data, and this already translates in a novel treatment paradigm.

Effects of acupuncture in treating insomnia due to spleen-stomach disharmony syndrome and its influence on intestinal microbiome: Study protocol for a randomized controlled trial

BackgroundInsomnia is a common complaint that is closely related to gastrointestinal symptoms, which is consistent with the traditional Chinese medicine classical theory of “stomach disharmony leading to restless sleep.” Acupuncture is an effective complementary and alternative medicine therapy to improve gastrointestinal function and restore the normal sleep-wake cycle. However, studies on the effectiveness of acupuncture for insomnia due to spleen-stomach disharmony syndrome are limited to case reports and few randomized controlled trials; deeper research on its mechanism is still lacking. This randomized controlled trial aims to assess the treatment efficacy of “harmonizing stomach to tranquilize mind” acupuncture for insomnia and its influence on the intestinal microbiome. Methods/designThis is a randomized, single-blind, parallel-group study. Sixty eligible patients with insomnia due to spleen-stomach disharmony syndrome will be randomly divided into two groups (1:1 allocation ratio). The intervention group will use “harmonizing stomach to tranquilize mind” acupuncture, and the control group will receive sham acupuncture. Participants will receive 5 acupuncture treatment sessions per week for 4 consecutive weeks. The Pittsburgh Sleep Quality Index will be used to evaluate the clinical efficacy of acupuncture treatment by making assessments at baseline, the end of treatment and the end of the follow-up. High-throughput 16S ribosomal ribonucleic acid gene sequencing will be performed to detect changes in the intestinal microbial composition before and after treatment. DiscussionThe results of this trial are expected to confirm that “harmonizing stomach to tranquilize mind” acupuncture can effectively relieve insomnia and alter the intestinal microbiome. Trial registrationChinese Clinical Trials Registry: ChiCTR1800017092.

Micrococcus aloeverae - A Rare Cause of Peritoneal Dialysis-Related Peritonitis Confirmed by 16S rRNA Gene Sequencing.

The number of patients receiving peritoneal dialysis has increased worldwide. Herein, we report the first case to our knowledge of continuous ambulatory peritoneal dialysis (CAPD) peritonitis caused by Micrococcus aloeverae, which was initially reported to be caused by Micrococcus luteus in the dialysate culture report but later identified by 16S ribosomal ribonucleic acid (rRNA) gene sequencing as M. aloeverae. A 59-year-old woman visited the emergency room due to abdominal pain. She was hospitalized with CAPD peritonitis. The patient initially responded to empirical antibiotic treatment comprising intraperitoneal cefazolin (15 mg/kg/day) and ceftazidime (1 g/day); however, the leukocyte count of dialysate effluent increased again. M. luteus was isolated four times from peritoneal dialysate cultures. We treated the patient with intraperitoneal administration of vancomycin (2 g loading, followed by 1 g every 7 days) but needed to switch from CAPD to temporary hemodialysis. We analyzed the 16S rRNA sequence to confirm the exact causative organism, and the results revealed that the organism was M. aloeverae. Because M. aloeverae and M. luteus have sequence similarity, 16S rRNA sequencing is a useful method to distingush them.

Effect of Resistant Starch on the Gut Microbiota and Its Metabolites in Patients with Coronary Artery Disease.

Aim: Bacteroides vulgatus and B. dorei have a protective effect against atherosclerosis, suggesting that expansion of these species in the gut microbiota could help patients with coronary artery disease (CAD). This study aimed to investigate the effect of resistant starch (RS) on the gut microbiota and its metabolites in fecal sample cultures from patients with CAD and individuals without CAD, using a single-batch fermentation system.Methods: Fecal samples from 11 patients with CAD and 10 individuals without CAD were fermented for 30 h with or without RS in the Kobe University Human Intestinal Microbiota Model (KUHIMM). Gut microbiota and the abundance of B. vulgatus and B. dorei were analyzed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing and the quantitative polymerase chain reaction. Short-chain fatty acids were analyzed using high-performance liquid chromatography.Results: Gut microbial analysis showed significantly lower levels of B. vulgatus and B. dorei in the original fecal samples from patients with CAD, which was simulated after 30 h of fermentation in the KUHIMM. Although RS significantly increased the absolute numbers of B. vulgatus and B. dorei, and butyrate levels in CAD fecal sample cultures, the numbers varied among each patient.Conclusions: The effect of RS on gut microbiota and its metabolites in the KUHIMM varied between CAD and non-CAD fecal sample cultures. The KUHIMM may be useful for preclinical evaluations of the effects of RS on the gut microbiota and its metabolites.

Longitudinal Analysis of Infant Stool Bacteria Communities Before and After Acute Febrile Malaria and Artemether-Lumefantrine Treatment.

BackgroundGut microbiota were recently shown to impact malaria disease progression and outcome, and prior studies have shown that Plasmodium infections increase the likelihood of enteric bacteria causing systemic infections. Currently, it is not known whether Plasmodium infection impacts human gut microbiota as a prelude to bacteremia or whether antimalarials affect gut microbiota. Our goal was to determine to what degree Plasmodium infections and antimalarial treatment affect human gut microbiota.MethodsOne hundred Kenyan infants underwent active surveillance for malaria from birth to 10 months of age. Each malaria episode was treated with artemether-lumefantrine (AL). Any other treatments, including antibiotics, were recorded. Stool samples were collected on an approximately biweekly basis. Ten children were selected on the basis of stool samples having been collected before (n = 27) or after (n = 17) a malaria episode and without antibiotics having been administered between collections. These samples were subjected to 16S ribosomal ribonucleic acid gene (V3–V4 region) sequencing.ResultsBacterial community network analysis revealed no obvious differences in the before and after malaria/AL samples, which was consistent with no difference in alpha and beta diversity and taxonomic analysis at the family and genus level with one exception. At the sequence variant (SV) level, akin to bacterial species, only 1 of the top 100 SVs was significantly different. In addition, predicted metagenome analysis revealed no significant difference in metagenomic capacity between before and after malaria/AL samples. The number of malaria episodes, 1 versus 2, explained significant variation in gut microbiota composition of the infants.ConclusionsIn-depth bioinformatics analysis of stool bacteria has revealed for the first time that human malaria episode/AL treatment have minimal effects on gut microbiota in Kenyan infants.

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats.

A high-salt diet is considered a cardiovascular risk factor; however, the mechanisms are not clear. Research suggests that gut bacteria-derived metabolites such as trimethylamine N-oxide (TMAO) are markers of cardiovascular diseases. We evaluated the effect of high salt intake on gut bacteria and their metabolites plasma level. Sprague Dawley rats ages 12-14 wk were maintained on either water (controls) or 0.9% or 2% sodium chloride (NaCl) water solution (isotonic and hypertonic groups, respectively) for 2 wk. Blood plasma, urine, and stool samples were analyzed for concentrations of trimethylamine (TMA; a TMAO precursor), TMAO, and indoxyl sulfate (indole metabolite). The gut-blood barrier permeability to TMA and TMA liver clearance were assessed at baseline and after TMA intracolonic challenge test. Gut bacterial flora was analyzed with a 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis. The isotonic and hypertonic groups showed a significantly higher plasma TMAO and significantly lower 24-hr TMAO urine excretion than the controls. However, the TMA stool level was similar between the groups. There was no significant difference between the groups in gut-blood barrier permeability and TMA liver clearance. Plasma indoxyl concentration and 24-hr urine indoxyl excretion were similar between the groups. There was a significant difference between the groups in gut bacteria composition. High salt intake increases plasma TMAO concentration, which is associated with decreased TMAO urine excretion. Furthermore, high salt intake alters gut bacteria composition. These findings suggest that salt intake affects an interplay between gut bacteria and their host homeostasis.