Metagenomic analysis of mycobacterial transrenal DNA in patients with HIV and tuberculosis coinfection.

The existence of "transrenal" DNA (tr-DNA), i.e. cell-free DNA that has distributed through the renal barrier to the urine, was first shown from a pathogen in 2000 (Botezatu et al., 2000). However, a targeted search for tr-DNA from Mycobacterium tuberculosis (MBT) started relatively recently (Cannas et al., 2008; Green et al., 2009). While other MBT cellular components found in the urine, e.g. lipoarabinomannan, have been used as an enhanced diagnostic tool, tr-DNA has the potential for strain specific identification or a more persistent biomarker during treatment of active disease. We therefore sought to identify by high-throughput next generation sequencing (NGS) MBT genome fragments in the urine of people with human immunodeficiency virus and tuberculosis (HIV-TB) co-infection living in a co-epidemic setting, and to evaluate whether these DNA targets are suitable for the development a quantitative TaqMan polymerase chain reaction with real-time detection (rt-PCR). Selection and mapping to the reference MBT genome of strain H37Rv (NC_000962) revealed 158 fragments of mycobacterial DNA with length from 19 to 44 base pairs (bp) repeated in different DNA samples. Five targets were chosen for design of rt-PCR primers and probes. Comparative analysis of the newly developed tests that were based on the results of NGS did not reveal a significant increase in sensitivity and specificity relative to the previous empirically designed targets. Howver, highly reproducible NGS reads of mycobacterial tr-DNA were obtained. rt-PCR test development suitable for more practical clinical use was likely limited by the small size of the secreted DNA fragments. It is necessary to develop further molecular approaches for the detection of mycobacterial tr-DNA or rely on NGS techniques with inherent bioinformatics requirements.

Ionofore antibiotic polynactin produced by Streptomyces sp. 156A isolated from Lake Baikal.

The potential antibacterial activity of secondary metabolites produced by Streptomyces sp. 156A isolated from Lake Baikal was investigated. The selective liquid-liquid extraction method was applied to obtain a mixture of nactins (polynactin) produced by the strain. The polynactin consisted of nonactin (3%), monactin (18%), dinactin (36%), trinactin (31%) and tetranactin (12%). The compounds were identified by MS/MS, 1H and 13C NMR methods. The loss of neutral 184 and 198 Da fragments from a sodiated molecular ion, [M + Na]+, of nactins was observed in the MS/MS spectrum. The polynactin was shown to possess the antibiotic activity against Gram-positive strains including opportunistic strains and strains isolated from various ecosystems of Lake Baikal.

Activity of bacteria in water of hot springs from Southern and Central Kamchatskaya geothermal provinces, Kamchatka Peninsula, Russia.

The hot-spring waters of numerous hot springs at the Kamchatka Peninsula, Russia differ in their chemical characteristics and elemental composition. Total bacterial abundance (TBA) as well as enzymatically active and respiring bacteria was enumerated in water samples collected from the Nalychevskie, Oksinskie, Apapelskie, and Dachnye hot springs. 5-Carboxyfluorescein diacetate activity was detected in all water samples and comprised 29-65% of the TBA as determined by 4',6-diamidino-2-phenylindol staining. The respiratory activity of iron-oxidizing bacteria was assayed by 5-cyano-2,3-ditolyltetrazolium chloride reduction. Respiring cells accounted for 9-14% of the TBA, indicating a positive correlation with the number of iron-oxidizing bacteria from the hot-spring biomats. Enumeration of heterotrophic bacteria revealed a high-density bacterial population only in the water of the Apapelskie hot spring, which has a temperature of 36 degrees C. Therefore, it appears that heterotrophic and iron-oxidizing bacteria inhabiting the hot-spring waters are essential for the geochemical processes occurring in hydrothermal systems.

Fe-Si biominerals in the Vilyuchinskie hot springs, Kamchatka Peninsula, Russia.

The micromorphological structure of microbial mats (biomats) from the hot springs of the Vilyuchinskaya hydrothermal system, Kamchatka Peninsula, Russia, were investigated. The Vilyuchinskie hot springs had a discharge temperature of 55-56 degrees C and Na-Ca-HCO3-type waters rich in silicic and boric acids. Water and biomats had high concentrations of Fe, Mn, Sr, and As. Enumeration of total bacterial abundance (TBA) demonstrated a low density of bacterial populations. However, the fractions of metabolically active bacteria and respiring iron-oxidizing bacteria in the hot-spring water were high, comprising 68 and 21% of TBA, respectively. Scanning electron microscopy equipped with an energy dispersive X-ray spectrometer (SEM-EDX) showed that unicellular rod-shaped bacteria about 5-microm long predominated in the brown biomats. The mineral capsules of these bacteria contained large amounts of Fe and Si. Extracellular and intracellular particles were observed by transmission electron microscopy. Fe-oxidizing bacteria were isolated from the biomats on agar plates with selective medium. Therefore, it can be concluded that microorganisms inhabiting the biomats of the Vilyuchinskie hot springs are essential for the deposition of Fe-minerals at neutral pH.

Fe-Si biominerals in the Vilyuchinskie hot springs, Kamchatka Peninsula, Russia / Biominerales de Fe-Si de las fuentes termales de Vilyuchiskie, en la península de Kamchatka (Rusia)

The micromorphological structure of microbial mats (biomats) from the hot springs of the Vilyuchinskaya hydrothermal system, Kamchatka Peninsula, Russia, were investigated. The Vilyuchinskie hot springs had a discharge temperatureof 55–56°C and Na-Ca-HCO3-type waters rich in silicic and boric acids. Water and biomats had high concentrations of Fe, Mn, Sr, and As. Enumeration of total bacterial abundance (TBA) demonstrated a low density of bacterial populations. However, the fractions of metabolically active bacteria and respiring iron-oxidizing bacteria in the hot-spring water were high, comprising 68 and 21% of TBA, respectively. Scanning electron microscopy equipped with an energy dispersive X-rayspectrometer (SEM-EDX) showed that unicellular rod-shaped bacteria about 5-μm long predominated in the brown biomats. The mineral capsules of these bacteria contained large amounts of Fe and Si. Extracellular and intracellular particles were observed by transmission electron microscopy. Fe-oxidizing bacteria were isolated from the biomats on agar plates with selective medium. Therefore, it can be concluded that microorganisms inhabiting the biomats of the Vilyuchinskie hot springs are essential for the deposition of Fe-minerals at neutral pH (AU)

Se describe el estudio de la estructura micromorfológica de los tapetes microbianos (biomats) de las fuentes termales del sistema hidrotermal de Vilyunchinskaya, en la península de Kamchatka (Rusia). Las fuentes hidrotermales de Vilyichinskie tenían una temperatura de descarga de 55–56ºCy sus aguas son del tipo Na-Ca-HCO3, ricas en ácidos silícico y bórico. El aguay los tapetes microbianos tenían una alta concentración de Fe, Mn, Sr y As. La enumeración de la abundancia total de bacterias (ATB) mostró una baja densidad de poblaciones bacterianas. Sin embargo, en el agua de las fuentes termales las fracciones de bacterias metabólicamente activas y de bacterias respiradoras oxidadoras de Fe eran elevadas, del 68 y el 21% de ATB, respectivamente. El estudio mediante el microscopio electrónico de barrido equipado con un espectrofotómetro de rayos X dispersor de energía (SEM-EDX) mostró que en los tapetes microbianos marrones predominaban las bacterias unicelulares en forma de bacilo de unos 5 μm. Las cápsulas minerales de estas bacterias contenían gran cantidad de Fe y Si. La observación con microscopía electrónica de transmisión reveló la presencia de partículas extracelulares e intracelulares. De los tapetes microbianos se aislaron bacterias oxidadoras de Fe mediante placas de agar con medio selectivo. Por tanto, se puede concluir que los microorganismos de los tapetes microbianos de las fuentes termales de Vilyuchinskie son esenciales para el depósito de minerales de hierro a pH neutro (AU)