Comparison of the microbiota diversity between autogenous and anautogenous Culex pipiens pallens / 中国血吸虫病防治杂志

Objective To investigate the microbiota composition and diversity between autogenous and anautogenous Culex pipiens pallens, so as to provide insights into unraveling the pathogenesis of autogeny in Cx. pipiens pallens. Methods Autogenous and anautogenous adult Cx. pipiens pallens samples were collected at 25 ℃, and the hypervariable regions of the microbial 16S ribosomal RNA (16S rRNA) gene was sequenced on the Illumina NovaSeq 6000 sequencing platform. The microbiota abundance and diversity were evaluated using the alpha diversity index, and the difference in the microbiota structure was examined using the beta diversity index. The microbiota with significant differences in the abundance between autogenous and anautogenous adult Cx. pipiens pallens samples was identified using the linear discriminant analysis effect size (LEfSe). Results The microbiota in autogenous and anautogenous Cx. pipiens pallens samples belonged to 18 phyla, 28 classes, 70 orders, 113 families, and 170 genera, and the dominant phyla included Proteobacteria, Bacteroidetes, and so on. At the genus level, Wolbachia was a common dominant genus, and the relative abundance was (77.6 ± 11.3)% in autogenous Cx. pipiens pallens samples and (47.5 ± 8.5)% in anautogenous mosquito samples, while Faecalibaculum (0.4% ± 0.1%), Dubosiella (0.5% ± 0.0%) and Massilia (0.5% ± 0.1%) were specific species in autogenous Cx. pipiens pallens samples. Alpha diversity analysis showed that higher Chao1 index and ACE index in autogenous Cx. pipiens pallens samples than in anautogenous samples (both P values > 0.05), and lower Shannon index (P > 0.05) and Simpson index (P < 0.05) in autogenous Cx. pipiens pallens samples than in anautogenous samples. LEfSe analysis showed a total of 48 significantly different taxa between autogenous and anautogenous Cx. pipiens pallens samples (all P values < 0.05). Conclusion There is a significant difference in the microbiota diversity between autogenous and anautogenous Cx. pipiens pallens.

Molecular characteristics of clinically isolated Yersinia in Jiangsu Province from 2017 to 2021 / 中华地方病学杂志

Objective:To investigate the distribution and molecular characteristics of Yersinia isolated from diarrhea patients in Jiangsu Province. Methods:From 2017 to 2021, the stool samples of diarrhea patients were collected in Tongshan District of Xuzhou City and Dongtai City of Yancheng City, Jiangsu Province, where the national active monitoring sites of Yersinia enterocolitica, then Yersinia was isolated; meanwhile, suspected Yersinia strains were collected from sentinel hospitals in the province. The DNA of isolated strains was extracted for whole genome resequencing, and the data were uploaded to the EnteroBase database for Yersinia species identification; the original data were cleaned and processed for 16S ribosomal RNA (16S rRNA) gene polymorphism analysis. Five virulence genes (ail, ystA, ystB, yadA, virF) were scanned through the National Center for Biotechnology Information (NCBI) and Pathogen Virulence Factor Database (VFDB), and K-mer Tree was constructed and genomic characteristics were analyzed. Results:From 2017 to 2021, a total of 2 058 stool samples from diarrhea patients were collected, and 57 strains of Yersinia were isolated and identified; meanwhile, two Yersinia strains were collected from the sentinel hospital. Compared with EnteroBase database, 51 strains were identified as Yersinia enterocolitica, 4 strains as Yersinia proxima, 1 strain each as Yersinia aleksiciae, Yersinia massiliensis, Yersinia intermedia and Yersinia canariae. The 16S rRNA gene polymorphism analysis showed that all strains were clustered into 3 groups, which could distinguish Yersinia enterocolitica from other Yersinia. Among the 51 strains of Yersinia enterocolitica, 49 strains were virulence genotype Ⅲ(ail-, ystA-, ystB+, yadA-, virF-), two strains were virulence genotype Ⅱ(ail+, ystA+, ystB-, yadA-, virF-); and 8 other Yersinia strains were virulence genotype Ⅳ (ail-, ystA-, ystB-, yadA-, virF-). K-mer analysis could distinguish Yersinia enterocolitica from other Yersinia, JS-XZ-2020001 strain was far away from other Yersinia enterocolitica isolates, and serotype O8 strains were more concentrated. Conclusions:The clinical isolates of Yersinia enterocolitica from diarrhea patients are mainly Yersinia and other Yersinia co-exist in a small amount in Jiangsu Province, two new Yersinia species ( Yersinia proxima and Yersinia canariae) are discovered. The virulence genotype of Yersinia enterocolitica is mainly type Ⅲ. The 16S rRNA gene polymorphism analysis and K-mer analysis can effectively distinguish Yersinia enterocolitica from other Yersinia.

Analysis on the structural changes of intestinal and pulmonary flora in mice with sepsis and acute lung injury / 中华急诊医学杂志

Objective:To investigate the microecological structure changes and correlation in blood, lung tissue and fecal intestine of mice with sepsis and acute lung injury.Methods:A total of 12 healthy male C57BL/6J mice were divided into the cecal ligation and perforation (CLP) group and sham operation (sham) group by random number table method, with six mice in each group. In the CLP group, acute lung injury model of sepsis mice was prepared by CLP method. In the sham group, only laparotomy but no perforation of cecal ligation was performed. Eye blood, lung tissue, and feces were collected from mice in each group 24 h after surgery. Lung tissue morphological changes were observed by HE staining, and 16s ribosome RNA sequencing was used to analyze the structural changes of microecology of the bacterial flora at each site in sepsis mice and find out the correlation.Results:(1) HE staining showed that mice in the CLP group had exudation into the alveolar cavity of the lung, disordered lung tissue structure, accompanied by a large number of inflammatory cell infiltration, and the lung histopathological score was significantly higher than that in the sham group ( P < 0.01). (2)α diversity analysis showed that there was no statistical significance in blood and fecal samples between the sham group and CLP group, while Ace index, Chao index and Simpson index in lung tissue samples were statistically significant ( P < 0.05). (3) β diversity analysis showed that the differences in blood and fecal samples were greater between the sham group and CLP group than that within the group, and analysis of Bray Curtis, weighted, and unweighted indexes were statistically significant ( P < 0.05). (4) At the phylum level, compared with the sham group, the abundance of Proteobacteria gradually increased, and the abundance of Firmicutes and actinobacteria was decreased in the CLP group. At the genus level, the sham group was dominated by Acinetobacter and Duchenne, while the CLP group was dominated by Escherichia coli and unclassified Enterobacter. Blood flora was more similar to lung tissue flora composition as compared with fecal flora. Conclusions:The distribution of bacterial flora in blood, lung tissue and intestine of sepsis mice with acute lung injury is partially overlapped.

Effects of Ganbao capsules on intestinal mucosal barrier and gut microbiota in rats with non-alcoholic fatty liver disease / 中国药房

OBJECTIVE To study the effects of Ganbao capsules on intestinal mucosal barrier and gut microbiota in rats with non-alcoholic fatty liver disease （NAFLD）， and to explore its mechanism of prevention and treatment of NAFLD. METHODS Eight of 26 SD rats were randomly selected as blank group and fed with ordinary diet， and the remaining 18 rats were fed with high diet to establish NAFLD model （2 for modeling inspection）； after successful modeling， they were divided into model group and Ganbao group， with 8 rats in each group. Ganbao group were given Ganbao capsules solution （1 440 mg/kg） intragastrically， and the blank group and model group were given the constant volume of distilled water intragastrically， once a day， for consecutive 5 weeks. The contents of alanine aminotransferase （ALT）， aspartate aminotransferase （AST） and triglyceride （TG） in serum of rats were detected by automatic analyzer； the contents of lipopolysaccharide， tumor necrosis factor-α （TNF-α）， interleukin-6 （IL-6） and IL-1β in serum of rats were detected by enzyme-linked immunosorbent assay. The pathological morphology of liver and ileum tissues were observed by HE staining， the expressions of Occludin and zonula occludens-1 （ZO-1） were detected by immunohistochemistry method， and the intestinal flora were detected by 16S ribosomal RNA gene sequencing technology. RESULTS Compared with the model group， the serum contents of ALT， AST， TG， lipopolysaccharide， TNF-α， IL-6 and IL-1β in Ganbao group were decreased significantly （P＜0.01）， the pathological changes of liver and ileum tissues were improved 262 significantly， and the expressions of Occludin and ZO-1 were increased significantly （P＜0.01）. Intestinal microbiotaanalysis revealed that compared with the model group， Ganbao capsules could recover the abundance and diversity of the gut E-mail：hdf8833@126.com microbiota in rats. At the phylum level， Ganbao capsules could significantly increase the relative abundance of Bacteroidetes， and significantly reduce the relative abundance of Firmicutes and the ratio of Firmicutes to Bacteroidetes （P＜0.01）. At the genus level， Ganbao capsules could significantly increase the relative abundance of Lactobacillus， Blautia， Bacteroides and Akkermansia， and significantly reduce the relative abundance of Prevotella， Turicibacter， Weissella， SMB53 and Desulfovibrio （P＜0.05 or P＜0.01）. There were different species among the gut microbiota of rats in each group. CONCLUSIONS Ganbao capsules may improve NAFLD by protecting intestinal mucosal barrier function and regulating gut probiotics/harmful bacteria structure.

Bacterial community diversity in Dermatophagoides farinae using high-throughput sequencing / 中国血吸虫病防治杂志

Objective To investigate the bacterial community diversity in Dermatophagoides farinae. Methods Laboratory-cultured D. farinae was collected, and the composition of microbial communities was determined by sequence analyses of the V4 region in the bacterial 16S ribosomal RNA (16S rRNA) gene on an Illumina PE250 high-throughput sequencing platform. Following quality control and filtering of the raw sequence files, valid reads were obtained and subjected to operational taxonomic units (OTU) clustering and analysis of the composition of microbial communities and alpha diversity index using the Usearch software, Silva database, and Mothur software. Results A total of 187 616 valid reads were obtained, and 469 OTUs were clustered based on a sequence similarity of more than 97%. OTU annotation showed that the bacteria in D. farinae belonged to 26 phyla, 43 classes, 100 orders, 167 families and 284 genera. The bacteria in D. farinae were mainly annotated to five phyla of Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota, with Proteobacteria as the dominant phylum, and mainly annotated to five dominant genera of Ralstonia, norank-f-Mitochondria, Staphylococcus and Sphingomonas, with Wolbachia identified in the non-dominant genus. Conclusions A high diversity is identified in the composition of the bacterial community in D. farinae, and there are differences in bacterial community diversity and abundance among D. farinae.

Effects of noise exposure on structure and functional prediction of intestinal microbiota in rats / 环境与职业医学

Background Noise 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. Objective To investigate the effects of noise exposure on the structure of rat gut microbiota and to make predictions of gut microbiota function. Methods Male 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. Results Significant 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<0.05) and Peptococcaceae_unclassified (P<0.01) at the genus level were significantly higher in the NE_105dB group, and the relative abundance of Parasutterella (P<0.05) was significantly higher in the NE_95dB group compared to the control group. In addition, the Ruminococcaceae_NK4A214_group (P<0.05) was also significantly higher in the NE_105dB group compared to the NE_95dB group. The PICRUSt functional prediction analysis results showed that there were eight differential pathways between the control group and the NE_95dB group, in which D-arginine and D-ornithine metabolism, ascorbate and aldarate metabolism, carotenoid biosynthesis, glycerophospholipid metabolism, mineral absorption, NOD-like receptor signaling pathway and non-homologous end-joining were significantly down-regulated, and nucleotide metabolism was significantly up-regulated. There were 38 differential pathways between the control group and the NE_105dB group. Among them, D-arginine and D-ornithine metabolism, and mineral absorption were the differential metabolic pathways in both noise exposure groups, and both were down-regulated relative to the control group. Conclusion Chronic noise exposure could alter structure of rat gut microbiota and may affect metabolic functions of multiple microbiota genes.

Investigación traslacional en microbioma (InTraMic): un área de interés común y creciente en el IMTIB, Hospital Italiano e Instituto Universitario / Translational research in microbiome (InTraMic): an area of common and growing interest at IMTIB, Hospital Italiano and Instituto Universitario

Se estima que aproximadamente 100 trillones de microorganismos (incluidos bacterias, virus y hongos) residen en el intestino humano adulto y que el total del material genético del microbioma es 100 veces superior al del genoma humano. Esta comunidad, conocida como microbioma se adquiere al momento del nacimiento a través de la flora comensal de la piel, vagina y heces de la madre y se mantiene relativamente estable a partir de los dos años desempeñando un papel crítico tanto en el estado de salud como en la enfermedad. El desarrollo de nuevas tecnologías, como los secuenciadores de próxima generación (NGS), permiten actualmente realizar un estudio mucho más preciso de ella que en décadas pasadas cuando se limitaba a su cultivo. Si bien esto ha llevado a un crecimiento exponencial en las publicaciones, los datos sobre las poblaciones Latinoamérica son casi inexistentes. La investigación traslacional en microbioma (InTraMic) es una de las líneas que se desarrollan en el Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). Esta se inició en 2018 con la línea de cáncer colorrectal (CCR) en una colaboración con el Colorectal Cancer Research Group del Leeds Institute of Medical Research en el proyecto Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents. A fines de 2019 se cumplió el objetivo de comprobar la factibilidad de la recolección, envío y análisis de muestras de MBF en 5 continentes, incluyendo muestras provenientes de la Argentina, Chile, India y Vietnam. Luego de haber participado de capacitaciones en Inglaterra, se ha cumplido con el objetivo de la etapa piloto, logrando efectivizar la recolección, envío y análisis metagenómico a partir de la secuenciación de la región V4 del ARNr 16S. En 2019, la línea de enfermedad de hígado graso no alcohólico se sumó a la InTraMic iniciando una caracterización piloto en el marco de una colaboración con el laboratorio Novartis. Los resultados de ese estudio, así como el de cáncer colorrectal, están siendo enviados a publicación. En 2020, con la incorporación de la línea de trasplante alogénico de células progenitoras hematopoyéticas, fue presentado un proyecto para un subsidio del CONICET que ha superado la primera etapa de evaluación. En el presente artículo se brinda una actualización sobre la caracterización taxonómica de microbioma y se describen las líneas de investigación en curso. (AU)

It is estimated that approximately 100 trillion microorganisms (including bacteria, viruses, and fungi) reside in the adult human intestine, and that the total genetic material of the microbiome is 100 times greater than that of the human genome. This community, known as the microbiome, is acquired at birth through the commensal flora of the mother's skin, vagina, and feces and remains relatively stable after two years, playing a critical role in both the state of health and in disease. The development of new technologies, such as next-generation sequencers (NGS), currently allow for a much more precise study of it than in past decades when it was limited to cultivation. Although this has led to exponential growth in publications, data on Latin American populations is almost non-existent. Translational research in microbiome (InTraMic) is one of the lines developed at the Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). This started in 2018 with the Colorectal Cancer Line (CRC) in a collaboration with the Colorectal Cancer Research Group of the Leeds Institute of Medical Research in the project "Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents". At the end of 2019, the objective of verifying the feasibility of collecting, sending and analyzing MBF samples on 5 continents, including samples from Argentina, Chile, India and Vietnam, was met. After having participated in training in England, the objective of the pilot stage has been met, achieving the collection, delivery and metagenomic analysis from the sequencing of the V4 region of the 16S rRNA. In 2019, the non-alcoholic fatty liver disease line joined InTraMic, initiating a pilot characterization in the framework of a collaboration with the Novartis laboratory. The results of that study, as well as that of colorectal cancer, are being published. In 2020, with the incorporation of the allogeneic hematopoietic stem cell transplantation line, a project was presented for a grant from the CONICET that has passed the first stage of evaluation. This article provides an update on the taxonomic characterization of the microbiome and describes the lines of ongoing research. (AU)

Comparison of 16S Ribosomal RNA Targeted Sequencing and Culture for Bacterial Identification in Normally Sterile Body Fluid Samples: Report of a 10-Year Clinical Laboratory Review

As 16S ribosomal RNA (rRNA)-targeted sequencing can detect DNA from non-viable bacteria, it can be used to identify pathogens from clinical samples even in patients pretreated with antibiotics. We compared the results of 16S rRNA-targeted sequencing and culture for identifying bacterial species in normally sterile body fluid (NSBF): cerebrospinal, pericardial, peritoneal and pleural fluids. Over a 10-year period, a total of 312 NSBF samples were evaluated simultaneously using 16S rRNA-targeted sequencing and culture. Results were concordant in 287/312 (92.0%) samples, including 277 (88.8%) negative and 10 (3.2%) positive samples. Of the 16 sequencing-positive, culture-negative samples, eight showed clinically relevant isolates that included Fusobacterium nucleatum subsp. nucleatum, Streptococcus pneumoniae, and Staphylococcus spp. All these samples were obtained from the patients pretreated with antibiotics. The diagnostic yield of 16S rRNA-targeted sequencing combined with culture was 11.2%, while that of culture alone was 6.1%. 16S rRNA-targeted sequencing in conjunction with culture could be useful for identifying bacteria in NSBF samples, especially when patients have been pretreated with antibiotics and when anaerobic infection is suspected.

Identificación molecular de bacterias en salud y enfermedad periodontal / Molecular identification of bacteria in healthy and diseased periodontium

RESUMEN El estudio de la microbiota bacteriana asociada con periodontitis es esencial para desarrollar herramientas de diagnóstico y eficacia en las terapias, por esta razón el objetivo de este estudio fue identificar bacterias asociadas con periodontitis. Nosotros amplificamos el gen 16S rARN por reacción en cadena de polimerasa (PCR) y secuenciamos para investigar y comparar muestras subgingivales obtenidas de individuos sanos y pacientes con periodontitis moderada y severa. Identificamos Stenotrophomonas maltophilia, Porphyromonas gingivalis, Pseudomonas sp., Fusobacterium nucleatum, Haemophilus sp., Aggregatibacter sp. y Prevotella intermedia. P. gingivalis y F. nucleatum se asociaron con ambas periodontitis y Aggregatibacter sp. se asoció con periodontitis severa. Los resultados presentados aquí podrían contribuir en la toma de decisiones clínicas de la periodontitis.

ABSTRACT The study of bacterial microbiota associated with periodontitis is essential to develop effective diagnostic tools and therapies. Hence, the aim of this study was to identify the bacteria associated with periodontitis. We used 16S rRNA gene amplification by polymerase chain reaction (PCR) and sequencing to identify and compare 80 subgingival samples from patients with healthy periodontium and patients with severe and moderate periodontitis. We identified the following bacteria: Stenotrophomonas maltophilia, Porphyromonas gingivalis, Pseudomonas sp., Fusobacterium nucleatum, Haemophilus sp., Aggregatibacter sp., and Prevotella intermedia. P. gingivalis and F. nucleatum were associated with both moderate and severe periodontitis, and Aggregatibacter sp. was associated with severe periodontitis. The results of this research can be useful in clinical decision-making for treatment of patients with periodontitis.

Linderae radix ethanol extract attenuates alcoholic liver injury via attenuating inflammation and regulating gut microbiota in rats

This study aimed to explore the influence of gut microbiota alterations induced by Linderae radix ethanol extract (LREE) on alcoholic liver disease (ALD) in rats and to study the anti-inflammatory effect of LREE on ALD through the lipopolysaccharide (LPS) toll-like receptor 4 (TLR4)-nuclear factor kappa B (NF-κB) pathway. ALD rat models were established by intragastric liquor [50% (v/v) ethanol] administration at 10 mL/kg body weight for 20 days. Rats were divided into six groups: normal group (no treatment), model group (ALD rats), Essentiale group (ALD rats fed with Essentiale, 137 mg/kg), and LREE high/moderate/low dose groups (ALD rats fed with 4, 2, or 1 g LREE/kg). NF-κB and LPS levels were evaluated. Liver pathological changes and intestinal ultrastructure were examined by hematoxylin and eosin staining and transmission electron microscopy. The gut microbiota composition was evaluated by 16S rDNA sequencing. Expression levels of TLR4 and CD68 in liver tissue, and occludin and claudin-1 in intestinal tissue were measured. LREE treatment significantly reduced NF-κB and LPS levels, improved liver pathological changes, and ameliorated intestinal ultrastructure injury. Meanwhile, LREE-fed groups showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than the rats in the model group. Administration of LREE suppressed TLR4 overexpression and promoted the expression of occludin and claudin-1 in intestine tissue. Thus, LREE could partly ameliorate microflora dysbiosis, suppress the inflammatory response, and attenuate liver injury in ALD rats. The protective effect of LREE might be related to the LPS-TLR4-NF-κB pathway.

The First Case of Otitis in Korea Caused by Brevibacterium otitidis

Brevibacterium spp. are gram-positive rods that are considered to be strictly nonpathogenic, and a very few cases of their infection in humans have been reported. In this study, we report a case of otitis caused by Brevibacterium otitidis. A 53-year-old woman, who visited the hospital, complained of symptoms, such as otorrhea from both ears, ear fullness, tinnitus, and hearing impairment, for several months. Ear discharge was cultured on blood agar for pathogen identification. Bacteria from the isolated colony were initially identified as Actinomyces odontolyticus by VITEK 2 (bioMerieux, France), whereas VITEK® MS (bioMerieux, France) identified them as Brevibacterium luteolum. Subsequently, bacteria from the isolated colony were confirmed as B. otitidis by 16S rRNA sequencing. Antimicrobial susceptibility testing confirmed their sensitivity to vancomycin and linezolid and resistance to clindamycin and penicillin. To our knowledge, this is the first reported case of otitis caused by B. otitidis in Korea.

Identificação de micro-organismos presentes em sistemas de biolixiviação de cobre a 35 e 50°C / Identifying microorganisms related to copper bioleaching at 35 and 50°C

RESUMO A biolixiviação de minérios de baixo teor e com elevado conteúdo de impurezas tem se mostrado alternativa importante para o aproveitamento destes, uma vez que a recuperação do metal por métodos pirometalúrgicos convencionais mostra-se economicamente inviável. A identificação e quantificação dos micro-organismos capazes de promover a biolixiviação mostram-se estratégicas para alcançar bons rendimentos no controle do processo e na recuperação de metais. Nesse sentido, as técnicas de biologia molecular são as ferramentas mais utilizadas para tal propósito. Este trabalho, utilizando técnicas de reação em cadeia da polimerase (PCR), polimorfismos de comprimento dos fragmentos de restrição (RFLP) e reação em cadeia da polimerase seguida de eletroforese em gel com gradiente desnaturante (PCR-DGGE), mostrou que a diversidade nas colunas de biolixiviação de cobre estudadas é baixa e que a temperatura é importante na manutenção de determinadas espécies, havendo predominância de Acidithiobacillus ferroxidans a 35°C e de Sulfobacillus thermosulfidooxidans a 50°C.

ABSTRACT Bioleaching is an alternative to pyrometallurgy for the production of metals from low-grade ores containing high level of impurities, once that live pyrometallurgical methods are economically unfeasible. The quantification and identification of those microorganisms related to bioleaching is an important strategy for process control and thus metal recovery. In this regard, molecular biology is one of the main techniques utilized for such objective. This study applied PCR, RFLP and PCR-DGGE techniques to show that the microbial diversity in copper bioleaching columns under investigation is low and the temperature is important to define the species found, with predominance of Acidithiobacillus ferroxidans, at 35°C and Sulfobacillus thermosulfidooxidans at 50°C.

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota

Abstract In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.

Characterization of multidrug-resistant Acinetobacter ssp. strains isolated from medical intensive care units in Cali - Colombia / Caracterización de cepas de Acinetobacter spp. resistentes a múltiples fármacos aisladas de unidades de cuidados intensivos en Cali - Colombia

Abstract Introduction: The extensive use of antibiotics has led to the emergence of multi-resistant strains in some species of the genus Acinetobacter. Objective: To investigate the molecular characteristics of multidrug-resistant of Acinetobacter ssp. strains isolated from 52 patients collected between March 2009 and July 2010 in medical intensive care units in Cali - Colombia. Methods: The susceptibility to various classes of antibiotics was determined by disc diffusion method, and the determination of the genomic species was carried out using amplified ribosomal DNA restriction analysis (ARDRA) and by sequencing of the 16s rDNA gene. Also, the genes of beta-lactamases as well as, integrases IntI1 and IntI2 were analyzed by PCR method. Results: The phenotypic identification showed that the isolates belong mainly to A. calcoaceticus- A. baumannii complex. All of them were multi-resistant to almost the whole antibiotics except to tigecycline and sulperazon, and they were grouped into five (I to V) different antibiotypes, being the antibiotype I the most common (50.0%). The percent of beta-lactamases detected was: blaTEM (17.3%), blaCTX-M (9.6%), blaVIM (21.2%), blaIMP (7.7%), blaOXA-58 (21.2%), and blaOXA-51 (21.2%). The phylogenetic tree analysis showed that the isolates were clustering to A. baumannii (74.1%), A. nosocomialis (11.1%) and A. calcoaceticus (7.4 %). Besides, the integron class 1 and class 2 were detected in 23.1% and 17.3% respectively. Conclusion: The isolates were identified to species A. baumanii mainly, and they were multiresistant. The resistance to beta-lactams may be by for presence of beta-lactamases in the majority of the isolates.

Resumen Introducción: El uso extensivo de antibióticos ha llevado a la emergencia de cepas multirresistentes en algunas especies del género Acinetobacter. Objetivo: Investigar las características moleculares de resistencia a múltiples fármacos de cepas aisladas de Acinetobacter spp. colectadas entre marzo de 2009 y julio de 2010 en 52 pacientes de unidades de cuidados intensivos en Cali - Colombia. Métodos: La susceptibilidad a diversas clases de antibióticos se determinó mediante el método de difusión de disco, y la determinación de la especie genómica se llevó a cabo usando un análisis de restricción de ADN ribosómico amplificado (ARDRA) y mediante la secuenciación del gen 16s de ADNr. Además, se analizaron por el método de PCR los genes de las beta-lactamasas, como también, las integrasas IntI1 e IntI2. Resultados: La identificación fenotípica mostró que los aislamientos pertenecen principalmente al complejo A. calcoaceticus - A. baumannii. Todos ellos eran multirresistentes a casi todos los antibióticos excepto tigeciclina y sulperazón, y se agruparon en cinco (I a V) antibitipos diferentes, siendo el antibiotipo I el más común (50%). El porcentaje de betalactamasas detectadas fue: blaTEM (17,3%), blaCTX-M (9,6%), blaVIM (21,2%), blaIMP (7,7%), blaOXA-58 (21,2%), blaOXA- 51 (21.2%). El análisis del árbol filogenético mostró que los aislados se agrupaban en A. baumannii (74.1%), A. nosocomialis (11.1%) y A. calcoaceticus (7.4%). Además, el integrón clase 1 y clase 2 se detectaron en 23.1% y 17.3% respectivamente. Conclusión: los aislamientos se identificaron principalmente como la especie A. baumanii, y fueron multirresistentes. La resistencia a los betalactámicos puede deberse a la presencia de betalactamasas en la mayoría de los aislamientos.

Characterization of Alkaliphilic Bacteria Isolated from Bauxite Residue in the Southern Region of Minas Gerais, Brazil

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.

Laboratory Identification of Leptotrichia Species Isolated From Bacteremia Patients at a Single Institution

We describe the laboratory identification of Leptotrichia species from clinical isolates collected over a six-year period. Five isolates from blood cultures were identified as Leptotrichia species. Gram stain showed large, fusiform, gram-negative or -variable bacilli. Identification based on biochemical testing was unsuccessful; however, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry proved to be a useful tool for identifying Leptotrichia species to the genus level. Species level identification was successfully achieved by using 16S ribosomal RNA gene sequencing.

First Case of Psychrobacter sanguinis Bacteremia in a Korean Patient / 대한임상미생물학회지

Psychrobacter sanguinis has been described as a Gram-negative, aerobic coccobacilli originally isolated from environments and seaweed samples. To date, 6 cases of P. sanguinis infection have been reported. A 53-year-old male was admitted with a generalized tonic seizure lasting for 1 minute with loss of consciousness and a mild fever of 37.8℃. A Gram stain revealed Gram-negative, small, and coccobacilli-shaped bacteria on blood culture. Automated microbiology analyzer identification using the BD BACTEC FX (BD Diagnostics, Germany) and VITEK2 (bioMérieux, France) systems indicated the presence of Methylobacterium spp., Aeromonas salmonicida, and the Moraxella group with low discrimination. The GenBank Basic Local Alignment Search Tool and an Ez-Taxon database search revealed that the 16S rRNA gene sequence of the isolate showed 99.30% and 99.88% homology to 859 base-pairs of the corresponding sequences of P. sanguinis, respectively (GenBank accession numbers JX501674.1 and HM212667.1). To the best of our knowledge, this is the first human case of P. sanguinis bacteremia in Korea. It is notable that we identified a case based on blood specimens that previously had been misidentified by a commercially automated identification analyzer. We utilized 16S rRNA gene sequencing as a secondary method for correctly identifying this microorganism.

Viability of Mycobacterium leprae in the environment and its role in leprosy dissemination.

Background: Leprosy, a chronic disease caused by Mycobacterium leprae, is a public health concern in certain countries, including India. Although the prevalence of the disease has fallen drastically over time, new cases continue to occur at nearly the same rate in many regions. Several endemic pockets have been observed in India and elsewhere. The precise dynamics of leprosy transmission are still not clearly understood. Both live bacilli as well as M. leprae DNA have been detected in the soil and water of endemic areas; they possibly play an important role in disease transmission. Aims: To study the occurrence of viable M. leprae in environmental samples collected from areas of residence of patients with active leprosy. Methods: The study was conducted on 169 newly diagnosed leprosy patients in Ghatampur, Uttar Pradesh, India. Soil and water samples were collected from their areas of residence using a standardized protocol. An equal number of soil and water samples were also collected from non-patient areas of the same or adjoining villages. The environmental samples collected from the patients surroundings were subjected to 16S ribosomal RNA gene analysis after obtaining informed consent. Results: About a quarter of the environmental samples collected from patient areas, (25.4% of soil samples and 24.2% of water samples) were found to be positive for specifi c 16S ribosomal RNA genes of M. leprae. Environmental samples collected from non-patient areas were all found negative for M. leprae 16S ribosomal RNA genes. Limitations: The major limitation of the study was that the sample size was small. Conclusion: The study demonstrated the presence of viable strains of M. leprae in skin smear samples of paucibacillary patients and multibacillary patients, as well as in the environmental samples obtained from around their houses. This could play an important role in the continued transmission of leprosy.

Bacteriemia por Anaerobiospirillum thomasii con desenlace fatal / Anaerobiopirillum thomasii bacteremia with gatal outcome

Anaerobiospirillum thomasii ha sido descrito como causante de diarrea en humanos, pero no se han informado bacteriemias asociadas a este organismo. En esta comunicación describimos el primer aislamiento de A. thomasii como causa de bacteriemia fatal en una paciente alcohólica

Anaerobiospirillum thomasii has been reported as a causative agent of diarrhea in humans; however no bacteremia associated with this pathogen has been described so far. We present here the first case of fatal A. thomasii bacteremia in an alcoholic patient

Clinical and Microbiological Characteristics of Six Staphylococcus pettenkoferi Isolates From Blood Samples

Coagulase-negative staphylococci (CoNS) are reported to be the leading cause of nosocomial bloodstream infections. Staphylococcus pettenkoferi is a novel member of CoNS that was first isolated from the human blood and bursitis wound in 2002. We have reported cases of 6 S. pettenkoferi strains isolated from blood specimens, including one pathogen and 5 contaminants and catheter colonizers. Brucker Biotyper (Brucker Daltonics, Bremen, Germany) and molecular typing with 16S rRNA gene sequencing confirmed the 6 isolates as S. pettenkoferi. The conventional phenotypic identification of these isolates is not reliable owing to their inconsistent biochemical characteristics. Five of the 6 isolates were found to be resistant to oxacillin, and all isolates showed susceptibility to vancomycin and linezolid. For accurate identification of this novel species, advanced methods by using Brucker Biotyper or molecular methods such as 16S rRNA gene sequencing are required.