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Background and Aim: Anaplasma platys is a dog pathogen that causes anaplasmosis in various hosts, including humans. It is a rickettsial pathogen that causes cyclic thrombocytopenia in primary canine recipients and is spread by the brown dog tick Rhipicephalus sanguineus. This study aimed to map the genetic sequences of Anaplasma spp. isolates comparable with those of different global locations and determine the infection status of Pshdar Kurdish shepherd dogs from three regions in Sulaymaniyah province who did not exhibit clinical indications for Anaplasma. Materials and Methods: A total of 75 dog blood samples were collected from the center of the Sulaymaniyah, Dukan, and Ranya districts in the Sulaymaniyah province and subjected to polymerase chain reaction to determine the 16S ribosomal RNA (16S rRNA) gene of A. platys. Results: Only two dogs (2.7%) were positive for A. platys. The 16S rRNA gene of A. platys was sequenced and registered in the National Center for Biotechnology Information GenBank with accession number OR467538. With four nucleotide changes, the sequence exhibited 99.72% similarity to strains identified as human infections and those found in recognized tick vectors. Conclusion: We conclude that the blood of Pshdar Kurdish shepherd dogs in the Sulaymaniyah region of Iraq contains a small number of A. platys. Moreover, the phylogenetic tree of the isolated species, A. platys, was significantly similar to other strains of A. platys found worldwide. In the Kurdistan region of Iraq, this study represents the first molecular detection of the 16S rRNA gene of A. platys. [ABSTRACT FROM AUTHOR]

The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.

Body fluid identification is an essential step in the forensic biology workflow that can assist DNA analysts in determining where to collect DNA evidence. Current presumptive tests lack the specificity that molecular techniques can achieve; therefore, molecular methods, including microRNA (miRNA) and microbial signature characterization, have been extensively researched in the forensic community. Limitations of each method suggest combining molecular markers to increase the discrimination efficiency of multiple body fluids from a single assay. While microbial signatures have been successful in identifying fluids with high bacterial abundances, microRNAs have shown promise in fluids with low microbial abundance (blood and semen). This project synergized the benefits of microRNAs and microbial DNA to identify multiple body fluids using DNA extracts. A reverse transcription (RT)‐qPCR duplex targeting miR‐891a and let‐7g was validated, and miR‐891a differential expression was significantly different between blood and semen. The miRNA duplex was incorporated into a previously reported qPCR multiplex targeting 16S rRNA genes of Lactobacillus crispatus, Bacteroides uniformis, and Streptococcus salivarius to presumptively identify vaginal/menstrual secretions, feces, and saliva, respectively. The combined classification regression tree model resulted in the presumptive classification of five body fluids with 94.6% overall accuracy, now including blood and semen identification. These results provide proof of concept that microRNAs and microbial DNA can classify multiple body fluids simultaneously at the quantification step of the current forensic DNA workflow. [ABSTRACT FROM AUTHOR]

The aim of this study was to assess the reliability of rapid antigen detection tests (RADT) for Streptococcus pyogenes (GAS) and Streptococcus pneumoniae on pleural fluid samples for diagnosis of parapneumonic effusion/empyema (PPE) and their potential for improving pathogen identification rates. Sixty-three pleural samples were included from 54 patients on which GAS and S. pneumoniae RADT (BinaxNOW), culture, 16S rRNA PCR, and S. pneumoniae–specific PCR were performed. GAS RADT showed a sensitivity of 95.2% and a specificity of 100%. Pneumococcal RADT showed a sensitivity of 100% and specificity of 88.6%. Both RADT increased the pathogen identification rate in PPE compared to culture. [ABSTRACT FROM AUTHOR]

The diagnosis of pulmonary nocardiosis remains challenging. Rapid detection of Nocardia is of primary importance for early diagnosis and precise treatment of nocardiosis. In this study, our objective was to develop and validate a new TaqMan real-time PCR (qPCR) assay for rapidly detecting Nocardia spp. in respiratory samples. Based on published sequence data, primers in a conserved region of the 16S rRNA gene and a probe within that region that was specific for Nocardia were designed. The distinction effect of the qPCR assay was assessed between Nocardia and other respiratory-associated bacteria. Furthermore, the specificity and sensitivity of the assay were evaluated in respiratory clinical samples (n = 205), compared to the results of 16S rRNA gene amplicon sequencing and clinical diagnosis. The qPCR assay exhibited high specificity, sensitivity, repeatability, and reproducibility. The limit of detection of standard plasmid DNA was 3 × 102 copies/mL. Additionally, the qPCR assay was applied to the direct detection of 205 clinical respiratory samples. The specificity and sensitivity of the qPCR were all 100% compared to 16S rRNA gene amplicon sequencing, as well as 98.4% and 100% compared to clinical diagnosis respectively. The qPCR yielded results within 3 h of sample processing, compared to several days for culture, significantly reducing turnaround time. The results suggest that the new qPCR assay developed in this study provides reliable and rapid detection of Nocardia spp. in the respiratory tracts and is expected to reduce the time required for diagnosing and treating nocardiosis. [ABSTRACT FROM AUTHOR]

Background: In cirrhosis, spontaneous bacterial peritonitis)SBP) is the most frequent infection. Rapid and precise identification of bacteria in clinical and scientific settings has been greatly aided by the 16S rRNA gene. Objective: Assessment of role of 16S rRNA gene in diagnosing SBP among cirrhotic ascitic cases. Patients and Methods: our study was done on 60 adults cirrhotic ascitic patients, classified to 2 groups: Group I (SBP group - 38): involved all cases with ascitic fluid PMNL = 250 cells/mm3, Group II (Non SBP group - 22): involved all cases with ascitic fluid PMNL < 250 cells/mm3. Ascitic fluid (AF) examination, bacterial culture and polymerase chain reaction (PCR) for detection of DNA were assessed among all cases. Results: Significantly greater levels of CRP were seen in the SBP group in comparison to the non-SBP group. Culture had sensitivity 53.3%, specificity 68.2%, PPV 70.5%, NPV 64.9 % and accuracy 60% for SBP diagnosis. PCR had sensitivity 94.7%, specificity 63.3%, PPV 81.8%, NPV 87.5% and accuracy 83.33% for SBP diagnosis Conclusion: Rapid and precise identification of AF infection is crucial for successful therapy, and polymerase chain reaction (PCR) detection of the 16s rRNA gene in ascitic fluid demonstrates this. [ABSTRACT FROM AUTHOR]

BackgroundNoise has multiple negative effects on the organism, and gut microbes are influenced by the environment and are closely associated with the development of diseases. Currently, the effects of chronic noise exposure on intestinal microbiota are poorly understood.ObjectiveTo investigate the effects of noise exposure on the structure of rat gut microbiota and to make predictions of gut microbiota function.MethodsMale Wistar rats (6 weeks old, 160-180 g) were randomly divided into control, NE_95dB, and NE_105dB groups, 10 rats in each group. Rats in the NE_95dB and the NE_105dB groups were exposed to noise at 95 dB sound pressure level (SPL) and 105 dB SPL, respectively, 4 h per day for consecutive 30 d, while the control group was exposed to background noise. Feces were collected after the last noise exposure for intestinal microbiota detection. Based on the 16S ribosomal RNA (rRNA) gene sequencing method, the diversity and structure of microbiota in rat intestinal contents were analyzed and compared. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to predict functions of the identified intestinal microbiota genes.ResultsSignificant differences were found in the microbial structure of the rat gut after the designed noise exposure. In the α diversity results, there was a statistically significant difference in the Chao1 index between the NE_95dB group and the NE_105dB group (P=0.02), while there were no statistically significant differences in the Shannon and Simpson indexes between the noise exposure groups and the control group (P>0.05). The β diversity analysis results showed significant differences in species abundance between the control group and the noise exposure groups (P=0.001). Further species analysis results showed that the relative abundances of the Ruminococcaceae_NK4A214_group (P

Background and Aim: The nasal cavity of a pig serves as an entry point and a habitat for the colonization of commensal microbes and pathogenic bacteria. Based on biochemical and serological tests, Streptococcus β-hemolytic Group C was identified as the Gram-positive bacteria, which resulted in the 1994 outbreak and death of thousands of pigs in Bali. Furthermore, this agent is zoonotic and frequently results in the development of meningitis lesions in the infected pig. Recently, a meningitis outbreak in humans was also reported after the consumption of pig-derived foods at Sibang Kaja, Badung-Bali. This study aimed to identify and characterize Gram-positive β-hemolytic organisms collected from nasal swab of pigs from the outbreak area, as well as to compare API Kit and 16S rRNA gene analysis methods. Materials and Methods: This study commenced with the cultivation of two isolates, Punggul Swab Nasal (PSN) 2 and PSN 19, which were characterized by β-hemolysis activity. These samples were then conventionally and molecularly identified using Kit API 20 Strep and 16S ribosomal RNA (rRNA) gene primers, respectively. Results: Using the Kit API 20 Strep, both isolates were identified as Enterococcus faecium, which was previously classified as Group D Streptococci. Based on the 16S rRNA gene sequencing, PSN 2 and PSN 19 were molecularly confirmed to have 99 and 98.1% similarities with E. faecium (NR042054), respectively. Furthermore, both isolates share the same clade in the phylogenetic tree analysis. Conclusion: Using Kit API 20 Strep and 16S rRNA gene analysis, the PSN 2 and PSN 9 Gram-positive isolates with β-hemolysis activity from pig nasal swabs were identified as E. faecium.

Molecular methods for body fluid identification have been extensively researched in the forensic community over the last decade, mostly focusing on RNA‐based methods. Microbial DNA analysis has long been used for forensic applications, such as postmortem interval estimations, but only recently has it been applied to body fluid identification. High‐throughput sequencing of the 16S ribosomal RNA gene by previous research groups revealed that microbial signatures and abundances vary across human body fluids at the genus and/or species taxonomic level. Since quantitative PCR is still the current technique used in forensic DNA analysis, the purpose of this study was to design a qPCR multiplex targeting the 16S gene of Bacteroides uniformis, Streptococcus salivarius, and Lactobacillus crispatus that can distinguish between feces, saliva, and vaginal/menstrual secretions, respectively. Primers and probes were designed at the species level because these bacteria are highly abundant within their respective fluid. The validated 16S triplex was evaluated in DNA extracts from thirty donors of each body fluid. A classification regression tree model resulted in 96.5% classification accuracy of the population data, which demonstrates the ability of this 16S triplex to presumptively identify these fluids with high confidence at the quantification step of the forensic workflow using minimal input volume of DNA extracted from evidentiary samples. [ABSTRACT FROM AUTHOR]

Abstract Background Ticks are obligate haematophagous ectoparasites of vertebrate hosts and transmit the widest range of pathogenic organisms of any arthropod vector. Seven tick species are known to feed on bare-nosed wombats (Vombatus ursinus), in addition to the highly prevalent Sarcoptes scabiei mite which causes fatal sarcoptic mange in most bare-nosed wombat populations. Little is known about the pathogens carried by most wombat ticks or how they may impact wombats and wombat handlers. Methods Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. Genomic DNA was extracted from a subsample, and following the amplification of the bacterial 16S rRNA gene V3–V4 hypervariable region, next-generation sequencing (NGS) on the Illumina MiSeq platform was used to assess the microbial composition. Results A total of 447 tick specimens were collected from 47 bare-nosed wombats between January 2019 and January 2020. Five species of ticks were identified comprising wombat tick Bothriocroton auruginans (n = 420), wallaby tick Haemaphysalis bancrofti (n = 8), bush tick Haemaphysalis longicornis (n = 3), common marsupial tick Ixodes tasmani (n = 12), and Australian paralysis tick Ixodes holocyclus (n = 4). Tick infestations ranged from one to 73 ticks per wombat. The wombat tick was the most prevalent tick species comprising 94% of the total number of samples and was present on 97.9% (46/47) of wombat hosts. NGS results revealed the 16S rRNA gene diversity profile was predominantly Proteobacteria (55.1%) followed by Firmicutes (21.9%) and Actinobacteria (18.4%). A species of Coxiella sharing closest sequence identity to Coxiella burnetii (99.07%), was detected in 72% of B. auruginans and a Rickettsiella endosymbiont dominated the bacterial profile for I. tasmani. Conclusions A new host record for H. longicornis is the bare-nosed wombat. One adult male and two engorged adult female specimens were found on an adult male wombat from Coolagolite in New South Wales, and more specimens should be collected to confirm this host record. The most prevalent tick found on bare-nosed wombats was B. auruginans, confirming previous records. Analysis of alpha-diversity showed high variability across both sample locations and instars, similar to previous studies. The detection of various Proteobacteria in this study highlights the high bacterial diversity in native Australian ticks.

In this study, the aim was to investigate the discriminatory power of molecular diagnostics based on mNGS and traditional 16S ribosomal RNA PCR among Nocardia species. A total of fourteen clinical isolates from patients with positive Nocardia cultures and clinical evidence were included between January 2017 and June 2020 in HeNan Provincial People’s Hospital. DNA extraction and 16S rRNA PCR were performed on positive cultures, and pathogens were detected by mNGS in these same samples directly. Among the 14 Nocardia isolates, four species were identified, and N. cyriacigeorgica (8 cases) is the most common species. Twelve of the 14 Nocardia spp. isolates were identified by the two methods, while two strains of N. cyriacigeorgica were not identified by mNGS. All tested isolates showed susceptibility to trimethoprim-sulfamethoxazole (SXT), amikacin and linezolid. Apart from Nocardia species, other pathogens such as Acinetobacter baumannii, Klebsiella pneumonia, Aspergillus, Enterococcus faecalis, Human herpesvirus, etc., were detected from the same clinical samples by mNGS. However, these different pathogens were considered as colonization or contamination. We found that it is essential to accurately identify species for determining antibiotic sensitivity and, consequently, choosing antibiotic treatment. 16S rRNA PCR was useful for identification of nocardial infection among species, while this technique needs the clinicians to make the pre-considerations of nocardiosis. However, mNGS may be a putative tool for rapid and accurate detection and identification of Nocardia, beneficial for applications of antimicrobial drugs and timely adjustments of medication.

In this study, the aim was to investigate the discriminatory power of molecular diagnostics based on mNGS and traditional 16S ribosomal RNA PCR among Nocardia species. A total of fourteen clinical isolates from patients with positive Nocardia cultures and clinical evidence were included between January 2017 and June 2020 in HeNan Provincial People's Hospital. DNA extraction and 16S rRNA PCR were performed on positive cultures, and pathogens were detected by mNGS in these same samples directly. Among the 14 Nocardia isolates, four species were identified, and N. cyriacigeorgica (8 cases) is the most common species. Twelve of the 14 Nocardia spp. isolates were identified by the two methods, while two strains of N. cyriacigeorgica were not identified by mNGS. All tested isolates showed susceptibility to trimethoprim-sulfamethoxazole (SXT), amikacin and linezolid. Apart from Nocardia species, other pathogens such as Acinetobacter baumannii, Klebsiella pneumonia, Aspergillus, Enterococcus faecalis, Human herpesvirus , etc., were detected from the same clinical samples by mNGS. However, these different pathogens were considered as colonization or contamination. We found that it is essential to accurately identify species for determining antibiotic sensitivity and, consequently, choosing antibiotic treatment. 16S rRNA PCR was useful for identification of nocardial infection among species, while this technique needs the clinicians to make the pre-considerations of nocardiosis. However, mNGS may be a putative tool for rapid and accurate detection and identification of Nocardia , beneficial for applications of antimicrobial drugs and timely adjustments of medication. [ABSTRACT FROM AUTHOR]

Background: Ticks are obligate haematophagous ectoparasites of vertebrate hosts and transmit the widest range of pathogenic organisms of any arthropod vector. Seven tick species are known to feed on bare-nosed wombats (Vombatus ursinus), in addition to the highly prevalent Sarcoptes scabiei mite which causes fatal sarcoptic mange in most bare-nosed wombat populations. Little is known about the pathogens carried by most wombat ticks or how they may impact wombats and wombat handlers. Methods: Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. Genomic DNA was extracted from a subsample, and following the amplification of the bacterial 16S rRNA gene V3–V4 hypervariable region, next-generation sequencing (NGS) on the Illumina MiSeq platform was used to assess the microbial composition. Results: A total of 447 tick specimens were collected from 47 bare-nosed wombats between January 2019 and January 2020. Five species of ticks were identified comprising wombat tick Bothriocroton auruginans (n = 420), wallaby tick Haemaphysalis bancrofti (n = 8), bush tick Haemaphysalis longicornis (n = 3), common marsupial tick Ixodes tasmani (n = 12), and Australian paralysis tick Ixodes holocyclus (n = 4). Tick infestations ranged from one to 73 ticks per wombat. The wombat tick was the most prevalent tick species comprising 94% of the total number of samples and was present on 97.9% (46/47) of wombat hosts. NGS results revealed the 16S rRNA gene diversity profile was predominantly Proteobacteria (55.1%) followed by Firmicutes (21.9%) and Actinobacteria (18.4%). A species of Coxiella sharing closest sequence identity to Coxiella burnetii (99.07%), was detected in 72% of B. auruginans and a Rickettsiella endosymbiont dominated the bacterial profile for I. tasmani. Conclusions: A new host record for H. longicornis is the bare-nosed wombat. One adult male and two engorged adult female specimens were found on an adult male wombat from Coolagolite in New South Wales, and more specimens should be collected to confirm this host record. The most prevalent tick found on bare-nosed wombats was B. auruginans, confirming previous records. Analysis of alpha-diversity showed high variability across both sample locations and instars, similar to previous studies. The detection of various Proteobacteria in this study highlights the high bacterial diversity in native Australian ticks. [ABSTRACT FROM AUTHOR]

The present study was planned to explore the relationship between soil chemistry with bacterial population of Bt and non-Bt cotton and their phenotypic and molecular characteristics. The pre-plant soil and rhizospheres of Bt and non-Bt cotton were collected and analyzed for some soil parameters and bacterial population. The bacterial isolates were analyzed for their morphological, biochemical, and molecular characteristics. Bacterial population showed a significant (p

Abstract Background Microbial culture-based investigations of inflamed tonsil tissues have previously indicated enrichment of several microorganisms such as Streptococcus, Staphylococcus and Prevotella. These taxa were also largely reflected in DNA sequencing studies performed using tissue material. In comparison, less is known about the response of the overall oral cavity microbiota to acute tonsillitis despite their role in human health and evidence showing that their compositions are correlated with diseases such as oral cancers. In addition, the influence of subject-specific circumstances including consumption of prescription antibiotics and smoking habits on the microbiology of acute tonsillitis is unknown. Methods We collected oral rinse samples from 43 individuals admitted into hospital for acute tonsillitis and 165 non-disease volunteers recruited from the public, and compared their microbial community compositions using 16S rRNA gene sequencing. We assessed the impact of tonsillitis, whether subjects were prescribed antibiotics, the presence of oral abscesses and their smoking habits on community composition, and identified specific microbial taxa associated with tonsillitis and smoking. Results Oral rinse community composition was primarily associated with disease state (tonsillitis vs non-tonsillitis) although its effect was subtle, followed by smoking habit. Multiple Prevotella taxa were enriched in tonsillitis subjects compared to the non-tonsillitis cohort, whereas the non-tonsillitis cohort primarily showed associations with several Neisseria sequence variants. The presence of oral abscesses did not significantly influence community composition. Antibiotics were prescribed to a subset of individuals in the tonsillitis cohort but we did not observe differences in community composition associated with antibiotics consumption. In both tonsillitis and non-tonsillitis cohorts, smoking habit was associated with enrichment of several Fusobacterium variants. Conclusions These findings show that the oral cavity microbial community is altered during acute tonsillitis, with a consistent enrichment of Prevotella during tonsillitis raising the possibility of targeted interventions. It also supports the possible link between smoking, Fusobacteria and oral cancers.

Abstract We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.

Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche.

Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibet Plateau and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefore, understanding the gut microbiota composition and function of wild asses can provide a theoretical for the situ conservation of wild animals in the future.In this study, we measured the dry matter digestion by the 4 molar hydrochloric acid (4N HCL) acid-insoluble ash method and analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA genes in V3–V4 regions. The results showed that the dry matter digestion in wild asses was significantly higher than in domestic donkeys (P

Pseudomonas cichorii is divided into two subclades based on the 16S ribosomal RNA gene sequence and core genome multilocus sequence typing. It was shown that subclade 2 strains utilize d -tartrate as a sole carbon source, whereas subclade 1 strains do not. Draft genome sequencing was performed with P. cichorii strains to identify d -tartrate utilization genes. By genome comparative and homology search studies, an ∼7.1-kb region was identified to be involved in d -tartrate utilization. The region is subclade 2 specific, and contains tarD and dctA genes, which encode a putative enzyme and transporter of d -tartrate, respectively. When the region was introduced into subclade 1 strains, the transformants were able to utilize d -tartrate. Partial fragments of tarD and dctA were amplified from all subclade 2 strains tested in this study by PCR using gene-specific primers, but not from subclade 1 strains. This is the first report on the genetic analysis of biochemical characteristics corresponding to a specific phylogenetic group in P. cichorii. [ABSTRACT FROM AUTHOR]

Background: Mycobacterial culture is the gold standard for the diagnosis of nontuberculous Mycobacterium (NTM) infections. However, this method is not suitable for detection of coinfection with different NTMs.Research Question: The goal of this study was to determine if clone library analysis of BAL fluid (BALF) was useful for detection of NTM phylotypes, including multiple NTM phylotypes, in pulmonary NTM infections.Study Design and Methods: BALF samples obtained from 120 patients with suspected pulmonary NTM infections were retrospectively evaluated by using the mycobacterial culture and clone library methods between July 2010 and August 2016.Results: In total, 55 (45.8%) patients were diagnosed as NTM positive according to results of mycobacterial culture, and 52 patients were NTM positive as determined by using the clone library method. Furthermore, 45 (86.5%) and seven (13.5%) patients exhibited a single phylotype (mono-phylotype group) and multiple phylotypes of NTM (multi-phylotype group), respectively. Compared with the mono-phylotype group, the multi-phylotype group had a significantly higher incidence of adverse chest CT findings (P = .048). In addition, 11 patients who were NTM negative according to results of BALF mycobacterial culture were determined to be NTM positive according to the clone library method. Six of these 11 patients were eventually diagnosed as NTM positive by using mycobacterial culture results within 6.2 ± 2.1 months following the initial sample collection.Interpretation: Coinfection multiple phylotypes could be associated with adverse clinical findings. In addition, patients who test positive for NTM genes but negative for mycobacterial culture may be diagnosed with NTM lung infection within 1 year of the initial sample collection. Further follow-up of these patients may facilitate early detection of NTM species. [ABSTRACT FROM AUTHOR]

Psychrobacter spp. are a Gram negative bacteria, aerobic, non-motile, small, with coccobacilli shape. Originally isolated from seaweed samples and marine environments. Recently considered as rare opportunistic human pathogens. Sixty -five years old women admitted to hospital with diabetic mellitus and stage 4 pressure ulcers (PU) with seizure and mild fever 37.9 °C. A gram staining of blood culture revealed gram negative bacteria have a cocobacilli shape. The VITEK2 system (bioMérieux) misidentify the isolate as Acinetobacter bumannii complex with low discrimination. The submission of the bacterial isolate to the GenBank BLAST search tool revealed that the Iraqi isolate show 100% homology with Psychrobacter sp. From china with accession number ID: MK205167.1, the next matches with Uncultured Psychrobacter sp. (ID: KF859544.1 China) Psychrobacter pulmonis(ID: KU364058.1, India), Psychrobacter pulmonis (ID: MH550129.1, China)with 99% similarity for each one. This Psychrobacter sp. was the first isolate from bacteremia patients in Iraq. The identification based on 16S rRNA gene sequence for precisely identify this bacteria that misidentified by VITEK2 system. [ABSTRACT FROM AUTHOR]

Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche. [ABSTRACT FROM AUTHOR]

Hyperglycemia is one of the metabolic characteristics of gestational diabetes mellitus (GDM). Considering that GDM is able to cause changes in the gut bacterial community and function in the mother's intestine compared with healthy pregnant women, we aimed to clarify the correlation between hyperglycemia and gut microbiota in a GDM mouse model. Mice were divided into four groups: CE0, GDME0, CE18, and GDME18. C and GDM represent the control (C) and GDM groups, while E0 and E18 represent early or late trimesters of embryo day 0 or 18, respectively. GDM mouse models were created by injecting streptozocin on embryo day 0. The gut microbiota was characterized using the Illumina MiSeq platform targeting the V3–4 region of the 16S rRNA. Operational taxonomic unit analysis revealed a significant difference between CE18 and CE0, in which Akkermansia and Prevotellaceae were more abundant in the early trimester group, CE0. Moreover, the Clostridiales_vadinBB60 group was more abundant, while Parasutterella was much lower in GDME18 than in CE18. The gut microbiota community structure correlated with the GDM state, and LEfSe and molecular ecological network analysis further confirmed these diversities. Our research shows that changes in the community structure of the gut microbiota from the early to late trimester correlate with the GDM state. Changes in the abundance of the probiotic bacteria Akkermansia, Prevotellaceae, and Parasutterella may be involved in the GDM state. [ABSTRACT FROM AUTHOR]

Aim: A number of reports have implicated the role of the symbiotic bacterial communities associated with toxic dinoflagellates in the biosynthesis of saxitoxin during harmful algal blooms (HABs). However, the exact mechanisms by which the bacteria facilitate toxin production remain inconclusive. The toxic dinoflagellate, Pyrodinium bahamense var. compressum, is the causative organism responsible for paralytic shellfish poisoning in the coastal waters of Sabah, and it is caused by the consumption of filter-feeding shellfish contaminated with the neurotoxin, saxitoxin. The present study aimed at characterizing the species diversity of symbiotic bacteria occurring within a monoalgal culture of P. bahamense var. compressum. Methodology and results: The total bacterial DNA was amplified using paired-end 16S community sequencing on the Illumina platform, targeting the V3-V4 region of the 16S ribosomal RNA gene. Bacteria were classified into 20 classes, 43 orders, 60 families, and 105 genera. A total of 10 phyla were present, where the major phylum was Proteobacteria (69.5%). The major genera were Pseudoruegeria (32%), Roseibium (16%), Hyphomonas (16%), Phaeobacter (7%), Lutimaribacter (5%) and Methylophaga (5%). This study showed that the previous method of assessing microbial diversity occurring in P. bahamense var. compressum has underestimated the actual species diversity. Conclusion, significance and impact of study: The high-throughput sequencing of the 16S metagenomes revealed hitherto unreported bacterial taxa associated with P. bahamense var. compressum. The findings of the present work will pave the way for further studies aimed at isolating and characterizing symbiotic bacteria that are likely to be associated with the biosynthesis of toxins. [ABSTRACT FROM AUTHOR]

Introduction: Bacterial pleuritis is one of the most important pleural and respiratory infectious diseases, in addition, there have been no reports describing the clinical characteristics of patients with bacterial pleuritis according to molecular methods. An accurate understanding of the clinical characteristics and etiology of bacterial pleuritis is an issue that must be addressed. Objectives: The aim of this study was to clarify the clinical characteristics of the bacterial species in bacterial pleuritis. Methods: Pleural effusion samples were obtained from 29 patients with bacterial pleuritis. The microbiota of pleural effusion samples was analyzed by clone library analysis using the 16S ribosomal RNA gene. Results: The phylotypes of Fusobacterium spp. (24.1%) were most frequently the predominant phylotypes, followed by those of Streptococcus anginosus group (SAG) (20.7%) and S. aureus (17.2%). The predominant phylotypes of obligate anaerobes, including the Fusobacterium spp., were detected in 11 of 29 patients (37.9%). Patients in the SAG group were significantly older and presented lower serum albumin levels than those in the obligate anaerobe and other bacterial groups. Patients from the obligate anaerobe group took longer to present symptoms, and therefore the diagnosis of pleuritis was also delayed, in comparison to patients in the other bacterial groups. Conclusions: Our results demonstrated that there were characteristic differences between patients in SAG, obligate anaerobe and other bacterial groups. Physicians may need to consider treatment strategy options based on the clinical characteristics of patients with bacterial pleuritis. [ABSTRACT FROM AUTHOR]

Schistosomiasis japonica is a water-borne trematode infection transmitted by different subspecies of Oncomelania hupensis. As parasites may either co-evolve or locally adapt with their hosts, snail diversity, as revealed by morphometric and genetic studies, may reflect parasite diversity and elucidate snail susceptibility and transmission patterns. This study aimed to compare isolates of O. h. quadrasi based on a 342-bp fragment of the 16S ribosomal RNA gene. O. h. quadrasi isolates were collected from nine provinces known to have S. japonicum in the Philippines, namely Cagayan Valley, Bohol, Negros Occidental, Leyte, Davao, Davao del Sur, Mindoro Oriental, Northern Samar, and Sorsogon. O. h. hupensis and O. h. nosophora isolates were also collected from China and Japan, respectively. The 16S ribosomal RNA gene of each specimen was amplified and sequenced. Phylogenetic and network analyses based on the 221 16S rRNA gene sequences revealed that O. h. quadrasi clustered as a distinct clade from the two other subspecies. Of the four identified haplotypes for O. h. quadrasi, two haplotypes were from Negros Oriental (Ohq2 and Ohq3), and one haplotype was from Bohol (Ohq4). The isolates from the remaining seven provinces shared a common haplotype (Ohq1). The current study was able to show the relationship among O. hupensis subspecies and demonstrate the limited ability of mitochondrial 16S ribosomal molecular marker in differentiating O. h. quadrasi geographic strains in the Philippines.

Keisuke Naito,1 Kei Yamasaki,1 Kazuhiro Yatera,1 Kentaro Akata,1 Shingo Noguchi,1 Toshinori Kawanami,1 Kazumasa Fukuda,2 Takashi Kido,1 Hiroshi Ishimoto,3 Hiroshi Mukae3 1Department of Respiratory Medicine, 2Department of Microbiology, University of Occupational and Environmental Health, Japan, Kitakyushu City, Fukuoka, 3Second Department of Internal Medicine, Nagasaki University School of Medicine, Nagasaki City, Nagasaki, Japan Abstract: Pulmonary emphysema is an important radiological finding in chronic obstructive pulmonary disease patients, but bacteriological differences in pneumonia patients according to the severity of emphysematous changes have not been reported. Therefore, we evaluated the bacteriological incidence in the bronchoalveolar lavage fluid (BALF) of pneumonia patients using cultivation and a culture-independent molecular method. Japanese patients with community-acquired pneumonia (83) and healthcare-associated pneumonia (94) between April 2010 and February 2014 were evaluated. The BALF obtained from pneumonia lesions was evaluated by both cultivation and a molecular method. In the molecular method, ~600 base pairs of bacterial 16S ribosomal RNA genes in the BALF were amplified by polymerase chain reaction, and clone libraries were constructed. The nucleotide sequences of 96 randomly selected colonies were determined, and a homology search was performed to identify the bacterial species. A qualitative radiological evaluation of pulmonary emphysema based on chest computed tomography (CT) images was performed using the Goddard classification. The severity of pulmonary emphysema based on the Goddard classification was none in 47.4% (84/177), mild in 36.2% (64/177), moderate in 10.2% (18/177), and severe in 6.2% (11/177). Using the culture-independent molecular method, Moraxella catarrhalis was significantly more frequently detected in moderate or severe emphysema patients than in patients with no or mild emphysematous changes. The detection rates of Haemophilus influenzae and Pseudomonas aeruginosa were unrelated to the severity of pulmonary emphysematous changes, and Streptococcus species – except for the S. anginosus group and S. pneumoniae – were detected more frequently using the molecular method we used for the BALF of patients with pneumonia than using culture methods. Our findings suggest that M. catarrhalis is more frequently detected in pneumonia patients with moderate or severe emphysema than in those with no or mild emphysematous changes on chest CT. M. catarrhalis may play a major role in patients with pneumonia complicating severe pulmonary emphysema. Keywords: clone library method, chronic obstructive pulmonary disease, Goddard classification, molecular method, microflora, phylotype, Moraxella catarrhalis

Bacterial meningitis is a life-threatening condition that requires quick and definitive diagnosis. Bacterial cultures from cerebrospinal fluid (CSF) return with a negative result as treatment with antimicrobials are sometimes started before sampling of CSF can be obtained which makes isolating the causative bacteria challenging. The value of Broad Range 16S Ribosomal RNA Gene Polymerase Chain Reaction / Sequencing of CSF (Br-PCR) can address this problem by amplifying and identifying any bacterial DNA present in a clinical sample.A 65-year-old female presented with rapid onset of high fevers, headache, chills and right hip pain. She had blood cultures drawn, unremarkable CSF analysis in the emergency department, and was discharged home. Ten hours later, she developed vomiting and altered mental status, returned to hospital and started on antimicrobials for gram negative bacteremia and emergently intubated with repeat lumbar puncture showed evidence of bacterial meningitis with pleocytosis and elevated opening pressures. Empiric antimicrobial therapy was started. All subsequent CSF microbiological stains, cultures, and molecular analyses were negative. The blood cultures grew Haemophilus influenzae and H. influenzae meningitis was presumed to be the cause. Therefore, Br-PCR on CSF was sent which detected Haemophilus species DNA. She received a 3-week course of ceftriaxone. After rehabilitation, she returned home without any significant neurological deficits. No relapse of meningitis at 4 months was noted.The application for Br-PCR in the setting of suspected bacterial meningitis with negative stains and cultures could improve a diagnostic algorithm for bacterial meningitis.

We report a case of rat-bite fever in a 94-year-old woman with Streptobacillus notomytis infection. We established an epidemiologic link between exposure to rats and human infection by performing nested PCRs that detected S. notomytis in the intraoral swab specimens obtained from rats captured in the patient’s house.

The present study was planned to explore the relationship between soil chemistry with bacterial population of Bt and non-Bt cotton and their phenotypic and molecular characteristics. The pre-plant soil and rhizospheres of Bt and non-Bt cotton were collected and analyzed for some soil parameters and bacterial population. The bacterial isolates were analyzed for their morphological, biochemical, and molecular characteristics. Bacterial population showed a significant (p < 0.05) positive correlation with clay content, electrical conductivity, organic matter, total nitrogen, and available phosphorus and potassium negative with correlation with pH. Bt cotton showed a non-significant effect on the soil parameters, significant decrease in bacterial population, change in the morphological and biochemical characteristics of rhizobacteria and replacement of four bacterial species with five new ones suggests the potential effect of Bt cotton on its rhizoflora. The rhizosphere of non-Bt cotton cultivated in the fertile agriculture field was found to be the best for bacterial growth. [ABSTRACT FROM AUTHOR]

The association between oral health and systemic disease is recognized in the literature. The present study aimed to clarify the association between oral bacteria on the tongue dorsum and factors associated with oral health and systemic disease in middle-aged and elderly patients. The association between bacterial numbers, oral health status and systemic disease was preliminarily investigated in 70 patients (mean age, 69.5 years; range, 45–92 years) who visited the Department of Oral Health, Hiroshima University Hospital (Hiroshima, Japan). The bacterial 16S ribosomal RNA gene was employed to quantitate bacterial numbers using real-time polymerase chain reaction (PCR). PCR was also performed to detect the DNA of periodontal disease-related bacteria. Oral bacterial numbers were marginally negatively correlated with moisture levels on the tongue surface [Spearman's rank correlation coefficient (R)=−0.131, P=0.28). Subjects with bleeding on probing (BOP) or a ≥4 mm probing depth (PD) exhibited higher Porphyromonas gingivalis (P. gingivalis)-positive rates (50.0 and 51.1%, respectively) than those without BOP or a <4 mm PD (39.5 and 30.4%, respectively). Subjects with medical histories of hypertension, diabetes, stroke and heart disease exhibited a trend toward higher P. gingivalis-positive rates than those without such disorders. These findings indicated that the tongue moisture level may be associated with bacterial numbers on the tongue surface, while P. gingivalis on the tongue surface may be associated with systemic and periodontal diseases. Further investigation in a larger number of participants is necessary to clarify the correlation between bacterial numbers and systemic disease. [ABSTRACT FROM AUTHOR]

Bacteria are ubiquitous in all marine habitats and can be beneficial or detrimental to the survival and growth of shellfish raised in aquaculture. To reduce the exposure of cultured shellfish to potential pathogens, antibiotics can be used. However, risks associated with this practice have led to the development of alternative techniques such as ultraviolet (UV) light exposure for seawater disinfection. In this study, we used 16S rRNA gene metabarcoding to measure the effect of low (50 mJoules/cm 2 ) and high (200 mJoules/cm 2 ) UV treatment of seawater on the bacterial communities present in hatchery rearing water and in Pacific oyster Crassostrea gigas larvae. 81 samples were collected between 13 and 29 March 2017 for high-throughput DNA sequencing of bacterial communities, including differentially-treated seawater, the microalgae fed to the oysters and oyster larvae (fertilized eggs, early veliger larval stage [D-larvae], and pre-settlement stage) samples. Differences in larval mortality between low and high UV treatments were also assessed. We found that the two UV treatments influenced the overall bacterial community diversity and affected its composition in both seawater and oyster larval samples. While alpha-diversity was mostly driven by the UV treatment, we found that the microbiome composition was primarily affected by temporal changes in the water source. Compared to the bacterial microbiome associated with seawater, the oyster larvae microbiome changed more significantly in response to both UV treatments and sampling dates with marked shifts in the dominant bacteria associated with fertilized eggs (class Gammaproteobacteria , families Rhodospirillaceae and Pelagibacteraceae ), the D-larvae (family A lteromonadaceae ), and the pre-settlement larvae (families Flavobacteriaceae and Rhodobacteraceae ). As larval development progressed, an increasingly complex bacterial community structure was observed. These bacterial community changes were likely driven by multiple factors, including the microbiome associated with microalgal cultures, which increased in complexity over time. Despite the clear response of bacterial communities to both low and high UV treatments, no significant effect was observed in relation to the oyster larval mortality rate. These results suggest that increasing the UV treatment to 200 mJoules/cm 2 , if required for more efficacious disinfection and biosecurity, would not be detrimental to Pacific oyster larval survival. Further research is required to increase understanding of the dynamics of functionally critical bacterial taxa and their successive roles in post-larval development of Pacific oysters. [ABSTRACT FROM AUTHOR]

Due to varying positive rates of polymerase chain reaction (PCR) amplification, interpretation of conventional PCR results for non‑infectious ascites remains problematic. The present study developed a highly sensitive PCR protocol and investigated the positive rate of PCR for the 16S ribosomal (r)RNA gene in non‑infectious ascites. Following the design of a new PCR primer pair for the 16S rRNA gene (800F and 1400R), the sequences of PCR products were analyzed and the lower limit for bacterial DNA detection evaluated. The positive rate of PCR for 16S rRNA gene in non‑infectious ascites was also evaluated. PCR with the primer pair amplified the genomic DNA of 16S rRNA genes of major disease‑causing bacterial strains. Additionally, PCR with this primer pair provided highly sensitive detection of bacterial genomic DNA (lower limit, 0.1 pg of template DNA). When DNA samples isolated from ascites were used, the 16S rRNA gene was amplified independently of the presence of bacterial infection. PCR products contained the genomic DNA fragments of multiple bacterial species. Bacterial genomic DNA can be amplified from all ascitic fluids using a highly sensitive PCR protocol. Careful attention is required to interpret the results based on simple amplification of 16S rRNA gene with conventional PCR. [ABSTRACT FROM AUTHOR]

The ruminal microbiota plays major roles in feed digestion. The composition and fermentation of the bacterial communities in 3 important ruminant species have been studied previously. Here, we extended this research to the effect of concentrate-to-forage ratios on ruminal bacterial communities in Tarim red deer ( Cervus elaphus yarkandensis). Different concentrate-to-forage ratios (2:8, 3:7, 4:6, and 5:5) were fed to Tarim red deer for 20 days. Ruminal bacterial communities were elucidated by 16S ribosomal RNA gene sequencing on an Illumina HiSeq 2500 platform. The microbial composition and biodiversity at the different concentrate-to-forage ratio levels were analyzed using clustering of operational taxonomic units based on 97% sequence identity, taxonomic classification at the phylum and genus levels, α diversity, and β diversity. Rumen microorganisms of deer fed a diet with a concentrate-to-forage ratio of 2:8 had the highest species diversity, followed by ratios of 3:7, 4:6, and 5:5. The community structure of the A1 and A2 samples and the A3 and A4 samples was similar. The bacterial composition appeared to be affected by diet, with a lower dietary concentrate level tending to increase the richness and diversity of ruminal bacteria in the rumen of Tarim red deer. [ABSTRACT FROM AUTHOR]

Gut microbiome dysbiosis plays a profound role in the pathogenesis of obesity and tributyltin (TBT) has been found as an environmental obesogen. However, whether TBT could disturb gut microbiome and the relationship between obesity induced by TBT exposure and alteration in gut microbiota are still unknown. In order to assess the association between them, mice were exposed to TBTCl (50 μg kg −1 ) once every three days from postnatal days (PNDs) 24 to 54. The results demonstrated that TBT exposure resulted in increased body weight gain, lager visceral fat accumulation and dyslipidemia in male mice on PND 84. Correspondingly, 16S rRNA gene sequencing revealed that TBT treatment decreased gut microbial species and perturbed the microbiome composition in mice. Furthermore, Pearson’s corelation coefficient analysis showed a significantly negative correlation between the body weight and the alpha diversity of gut microbiome. These results suggested that TBT exposure could induce gut microbiome dysbiosis in mice, which might contribute to the obesity pathogenesis. [ABSTRACT FROM AUTHOR]

ABSTRACT The aim of this study was to isolate and characterize bacterial strains from bauxite residue in the southern region of Minas Gerais, Brazil, by 16S rRNA gene sequencing and biochemical assays. Bacillus cohnii, Bacillus pseudofirmus, and Bacillus clarkii were identified among the isolates. The isolates were able to use a wide range of carbon sources and to grow at NaCl concentrations of up to 10%, temperatures from 10 to 40 °C, and pH from 7 to 10.5, producing a wide variety of organic acids. This is the first report on microbial composition of bauxite residue in Brazil.

Schistosomiasis japonica is a water-borne trematode infection transmitted by different subspecies of Oncomelania hupensis. As parasites may either co-evolve or locally adapt with their hosts, snail diversity, as revealed by morphometric and genetic studies, may reflect parasite diversity and elucidate snail susceptibility and transmission patterns. This study aimed to compare isolates of O. h. quadrasi based on a 342-bp fragment of the 16S ribosomal RNA gene. O. h. quadrasi isolates were collected from nine provinces known to have S. japonicum in the Philippines, namely Cagayan Valley, Bohol, Negros Occidental, Leyte, Davao, Davao del Sur, Mindoro Oriental, Northern Samar, and Sorsogon. O. h. hupensis and O. h. nosophora isolates were also collected from China and Japan, respectively. The 16S ribosomal RNA gene of each specimen was amplif ied and sequenced. Phylogenetic and network analyses based on the 221 16S rRNA gene sequences revealed that O. h. quadrasi clustered as a distinct clade from the two other subspecies. Of the four identif ied haplotypes for O. h. quadrasi, two haplotypes were from Negros Oriental (Ohq2 and Ohq3), and one haplotype was from Bohol (Ohq4). The isolates from the remaining seven provinces shared a common haplotype (Ohq1). The current study was able to show the relationship among O. hupensis subspecies and demonstrate the limited ability of mitochondrial 16S ribosomal molecular marker in differentiating O. h. quadrasi geographic strains in the Philippines. [ABSTRACT FROM AUTHOR]

The bacterial species of the genus Xenorhabdus in the family Enterobacteriaceae have a mutualistic association with steinernematid entomopathogenic nematodes (EPNs), which have been used as biological control agents against soil insect pests. In this study we present the genetic and phenotypic characterizations of the Xenorhabdus species isolated from steinernematid nematodes in Japan. The 18 Japanese Xenorhabdus isolates were classified into five bacterial species based on 16S ribosomal RNA (16S rRNA) gene sequences: Xenorhabdus bovienii, Xenorhabdus hominickii, Xenorhabdus indica, Xenorhabdus ishibashii, and Xenorhabdus japonica. There was no genetic variation between the 16S RNA sequences among the three X. ishibashii isolates, 0-0.1% variation among the five X. hominickii isolates, and 0-0.5% among the eight X. bovienii isolates. Phenotypic characterization demonstrated that representative isolates of the five bacterial species shared common characteristics of the genus Xenorhabdus, and only X. hominickii isolates produced indole. Symbiotic association and co-speciation of Xenorhabdus bacteria with Steinernema nematodes from Japan are discussed. [ABSTRACT FROM AUTHOR]

Campylobacter rectus is a member of the human oral flora and is associated with periodontal disease. We report the first case of severe acute otitis media (AOM) due to C. rectus in a previous healthy 15-year-old boy, which was confirmed by 16S ribosomal RNA gene sequencing. C. rectus is a possible causative pathogen of AOM. [ABSTRACT FROM AUTHOR]

Introduction This study compared the antibacterial effects of 1% sodium hypochlorite (NaOCl) and 2% chlorhexidine digluconate (CHX) during retreatment of teeth with apical periodontitis. Methods Root canal–treated teeth with apical periodontitis were randomly distributed into 2 groups. Bacteriological samples were taken from the canals before (S1) and after (S2) preparation using either NaOCl or CHX irrigation and after calcium hydroxide medication (S3); 16S ribosomal RNA gene-based real-time quantitative polymerase chain reaction was performed to quantify total bacteria, streptococci, and Enterococcus faecalis . Results Forty-nine teeth were available for analysis (NaOCl, n = 20; CHX, n = 29). Bacterial DNA occurred in all S1 samples, streptococci in 57% and E. faecalis in 6%. The total bacterial counts decreased from S1 to S2 in both groups ( P < .01) but were higher in S3 than S2 ( P < .01). Thirty-five percent of the teeth in the NaOCl group were positive in S2, decreasing to 20% in S3. In the CHX group, 41% were positive in S2, decreasing to 31% in S3. The bacterial load in S1 influenced the incidence of bacteria in S2 ( P < .01). Streptococci were significantly reduced in both groups, and E. faecalis was found in only 1 S2 sample and not in S3. No significant difference between NaOCl and CHX was found. Conclusions NaOCl and CHX both reduced bacterial counts and the number of infected canals. Intracanal medication with calcium hydroxide reduced the number of canals with persistent infection but resulted in overall larger bacterial counts in the cases positive for bacteria. The effectiveness of antimicrobial treatment can be influenced by the initial bacterial load. [ABSTRACT FROM AUTHOR]

Purpose: In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis.Methods: Literature focused on human microbiota research was reviewed and summarized.Results: Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes.Conclusions: Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health. [ABSTRACT FROM AUTHOR]