Mycolicibacterium nivoides sp. nov isolated from a peat bog

Culture-dependent identification of rare marine sediment bacteria from the Gulf of Mexico and Antarctica

Laboratory-viable cultivars of previously uncultured bacteria further taxonomic understanding. Despite many years of modern microbiological investigations, the vast majority of bacterial taxonomy remains uncharacterized. While many attempts have been made to decrease this knowledge gap, culture-based approaches parse away at the unknown and are critical for improvement of both culturing techniques and computational prediction efficacy. To this end of providing culture-based approaches, we present a multi-faceted approach to recovering marine environmental bacteria. We employ combinations of nutritional availability, inoculation techniques, and incubation parameters in our recovery of marine sediment-associated bacteria from the Gulf of Mexico and Antarctica. The recovered biodiversity spans several taxa, with 16S-ITS-23S rRNA gene-based identification of multiple isolates belonging to rarer genera increasingly undergoing phylogenetic rearrangements. Our modifications to traditional culturing techniques have not only recovered rarer taxa, but also resulted in the recovery of biotechnologically promising bacteria. Together, we propose our stepwise combinations of recovery parameters as a viable approach to decreasing the bacterial knowledge gap.

Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications

Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium's oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products' end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.

Implications of PM2.5 chemical composition in modulating microbial community dynamics during spring in Seoul

Particulate matter with an aerodynamic diameter of 2.5 μm or less (PM2.5) harbors a diverse microbial community. To assess the ecological dynamics and potential health risks associated with airborne microorganisms, it is crucial to understand the factors influencing microbial communities within PM2.5. This study investigated the influence of abiotic parameters, including air pollutants, PM2.5 chemical composition (water-soluble ions and organics), and meteorological variables, on microbial communities in PM2.5 samples collected in Seoul during the spring season. Results revealed a significant correlation between air pollutants and water-soluble ions of PM2.5 with microbial α-diversity indices. Additionally, air pollutants exerted a dominant effect on the microbial community structure, with stronger correlations observed for fungi than bacteria, whereas meteorological variables including temperature, pressure, wind speed, and humidity exerted a limited influence on fungal α-diversity. Furthermore, the results revealed specific water-soluble ions, such as SO42-, NO3-, and NH4+, as important factors influencing fungal α-diversity, whereas K+ negatively correlated with both microbial α-diversity. Moreover, PM2.5 microbial diversity was affected by organic compounds within PM2.5, with fatty acids exhibited a positive correlation with fungal diversity, while dicarboxylic acids exhibited a negative correlation with it. Furthermore, network analysis revealed direct links between air pollutants and dominant bacterial and fungal genera. The air pollutants exhibited a strong correlation with bacterial genera, such as Arthrospira and Clostridium, and fungal genera, including Aureobasidium and Cladosporium. These results will contribute to our understanding of the ecological dynamics of airborne microorganisms and provide insights into the potential risks associated with PM2.5 exposure.

A polyphasic molecular approach to characterize a collection of grapevine endophytic bacteria with bioprotective potential

AIMS

The work presented here was conducted to characterize the biodiversity of a collection of bacterial isolates, mainly wood endophytes, as part of a research project focused on exploring their bioprotective potential for postharvest biological control of fruits.

METHODS AND RESULTS

This work was the basis for the development of a tailored method combining 16S rDNA sequencing and Rep-PCR to differentiate the isolates and identify them to genus level or below. More than one hundred isolates obtained from wood and roots of different grapevine genotypes were cultured on appropriate growth media and then subjected to the specified multistep molecular identification.

CONCLUSIONS

We have obtained good dereplication for grapevine-endophytic bacteria, together with reliable genetic identification. Both are essential prerequisites to properly characterize a biome bank and, at the same time, beneficial prerequisites to subsequently perform a correct bioprotection assessment.

Description of Mycolicibacterium arenosum sp. nov. Isolated from Coastal Sand on the Yellow Sea Coast

A Gram-staining-positive, aerobic, non-spore-forming bacterium was isolated from coastal sand samples from Incheon in the Republic of Korea and designated as strain CAU 1645T. The optimum conditions for growth were observed at 30 °C in growth media containing 1% (w/v) NaCl at pH 9.0. The predominant respiratory quinone was MK-9 and the major fatty acids were C16:0, C17:1 w7c, and summed feature 7. Similarly, the 16S rRNA gene sequence exhibited the highest similarity with Mycolicibacterium bacteremicum DSM 45578T and Mycolicibacterium neoaurum JCM 6365T, both of which exhibited similarity rates of 97.2%. The genomic DNA G+C content was 68.2%. The whole genome of strain CAU 1645T was obtained and annotated with annotation using RAST server. The pan-genome analysis was determined using Prokka, Roary, and Phandango. In the pan-genome analysis, the strain CAU 1645T shared 40 core genes with closely related Mycolicibacterium species, including the AcpM gene, the meromycolate extension acyl carrier protein involved in forming impermeable cell walls in mycobacteria. Therefore, our findings demonstrated that the isolate represents a novel species of the genus Mycolicibacterium, for which we propose the name Mycolicibacterium arenosum sp. nov. The type strain is CAU 1645T (= KCTC 49724T = MCCC 1K07087T).

Phylogenetic distribution of malonate semialdehyde decarboxylase (MSAD) genes among strains within the genus Mycobacterium: evidence of MSAD gene loss in the evolution of pathogenic mycobacteria

Despite the great diversity of malonate semialdehyde decarboxylases (MSADs), one of five subgroups of the tautomerase superfamily (TSF) found throughout the biosphere, their distribution among strains within the genus Mycobacterium remains unknown. In this study, we sought to investigate the phylogenetic distribution of MSAD genes of mycobacterial species via genome analysis of 192 different reference Mycobacterium species or subspecies retrieved from NCBI databases. We found that in a total of 87 of 192 strains (45.3%), MSAD-1 and MSAD-2 were distributed in an exclusive manner among Mycobacterium species except for 12 strains, including Mycobacterium chelonae members, with both in their genome. Of note, Mycobacterium strains better adapted to the host and of high virulence potential, such as the Mycobacterium tuberculosis complex, Mycobacterium leprae, Mycobacterium marinum, Mycobacterium ulcerans, and Mycobacterium avium subsp. paratuberculosis, had no orthologs of MSAD in their genome, suggesting MSAD loss during species differentiation in pathogenic slow-growing Mycobacterium. To investigate the MSAD distribution among strains of M. avium subspecies, the genome sequences of a total of 255 reference strains from the four subspecies of M. avium (43 of subspecies avium, 162 of subspecies hominissuis, 49 of subspecies paratuberculosis, and 1 of subspecies silvaticum) were further analyzed. We found that only 121 of 255 strains (47.4%) had MSADs in their genome, with none of the 49 M. avium subsp. paratuberculosis strains having MSAD genes. Even in 13 of 121 M. avium strains with the MSAD-1 gene in their genome, deletion mutations in the 98th codon causing premature termination of MSAD were found, further highlighting the occurrence of MSAD pseudogenization during species or subspecies differentiation of M. avium. In conclusion, our data indicated that there are two distinct types of MSADs, MSAD-1 and MSAD-2, among strains in the Mycobacterium genus, but more than half of the strains, including pathogenic mycobacteria, M. tuberculosis and M. leprae, have no orthologs in their genome, suggesting MSAD loss during host adaptation of pathogenic mycobacteria. In the future, the role of two distinct MSADs, MSAD-1 and MSAD-2, in mycobacterial pathogenesis or evolution should be investigated.

Rapid and Comprehensive Identification of Nontuberculous Mycobacteria

Next-generation sequencing is a powerful tool to accurately identify pathogens. The MinION sequencer is best suited for the rapid identification of bacterial species due to its real-time sequence output. In this chapter, we introduce a method to identify nontuberculous mycobacteria (NTM) in one sequencing analysis from culture isolates using the MinION sequencer. NTM disease is now recognized as a growing global health concern due to its increasing incidence and prevalence. There are over 200 NTM species, of which the major pathogens are further classified into many subspecies showing different antibiotic susceptibilities. Therefore, identifying the pathogens at the subspecies level of NTM is necessary to select an appropriate treatment regimen. The protocol described here includes DNA extraction by lysis using silica beads, library preparation, sequencing by the MinION sequencer, and analysis of multilocus sequence typing using the software "mlstverse" and enables rapid and comprehensive identification of 175 species of NTM at the subspecies level with high sensitivity and accuracy.

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

BACKGROUND

In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS

Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS

The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.