Williamsia spp. are emerging opportunistic bacteria

Gut Microbial Adaptation to Varied Altitudes and Temperatures in Tibetan Plateau Yaks

The yak (Bos grunniens) exhibits exceptional regional adaptability, enabling it to thrive in the distinctive ecological niches of the Qinghai-Tibet Plateau. Its survival relies on the intricate balance of its intestinal microbiome, essential for adapting to harsh environmental conditions. Despite the documented significance of bacteria and fungi in maintaining intestinal homeostasis and supporting immune functions, there is still a substantial gap in understanding how the composition and functionality of yak gut microbiota vary along altitude-temperature gradients. This study aims to fill this gap by employing 16S rRNA and ITS amplicon sequencing techniques to analyze and compare the intestinal microbiome of yaks residing at different elevations and exposed to varying temperatures. The findings demonstrate subtle variations in the diversity of intestinal bacteria and fungi, accompanied by significant changes in taxonomic composition across various altitudes and temperature gradients. Notably, Firmicutes, Actinobacteriota, and Bacteroidota emerged as the dominant phyla across all groups, with Actinobacteriota exhibiting the highest proportion (35.77%) in the LZF group. Functional prediction analysis revealed significant associations between the LZF group and metabolic pathways related to amino acid metabolism and biosynthesis. This suggests a potential role for actinomycetes in enhancing nutrient absorption and metabolism in yaks. Furthermore, our findings suggest that the microbiota of yaks may enhance energy metabolism and catabolism by modulating the Firmicutes-to-Bacteroidota ratio, potentially mitigating the effects of temperature variations. Variations in gut bacterial and fungal communities among three distinct groups were analyzed using metagenomic techniques. Our findings indicate that microbial genera exhibiting significant increases in yaks at lower altitudes are largely beneficial. To sum up, our research investigated the changes in gut bacterial and fungal populations of yaks residing across diverse altitude and temperature ranges. Moreover, these results enhance comprehension of gut microbial makeup and variability, offering perspectives on the environmental resilience of dry lot feeding yaks from a microbial angle.

Williamsia muralis bacteraemia in a patient with Fanconi anaemia after haematopoietic cell transplantation

Introduction

Williamsia muralis is an environmental bacterium first detected in 1999. Infections with W. muralis isolated have been reported in two elderly patients, and were associated with the surgical intervention of artificial objects. We present a case of bacteraemia caused by W. muralis following haematopoietic cell transplantation (HCT).

Case presentation

A 10-year-old Japanese boy presented with fever and the swelling of the left cheek 8 days after HCT for the treatment of Fanconi anaemia. Gram-positive, rod-shaped bacteria were isolated from the blood cultures after 5 days incubation. 16S rRNA sequencing, but not mass spectrometry, identified a strain of W. muralis (1 414 bp, %ID 100 %). The phlegmon did not respond to antimicrobial therapy, but remitted with defervescence after a successful engraftment with teicoplanin and meropenem therapy on day 16 after HCT. The patient experienced recurrence of the bacteraemia, leading to central venous catheter (CVC) line removal. The same strain of W. muralis was isolated from the cultured tip of the CVC. To our knowledge, this is the first reported case of W. muralis bacteraemia and was complicated by CVC infection after HCT.

Conclusion

W. muralis bacteraemia developed in an immunocompromised child. Introduction of artificial objects into the body raises a risk of rare infection with slowly growing environmental bacteria.

Cross-alteration of murine skin and tick microbiome concomitant with pathogen transmission after Ixodes ricinus bite

BACKGROUND

Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essential during the process of tick feeding and for the mechanism of pathogen transmission. However, it has been poorly investigated.

METHODS

We used mice bitten by field-collected ticks (nymphs and adult ticks) in different experimental conditions to investigate, by 16S rRNA gene metabarcoding, the impact of blood feeding on both the mouse skin microbiome and the tick microbiome. We also investigated by PCR and 16S rRNA gene metabarcoding, the diversity of microorganisms transmitted to the host during the process of tick bite at the skin interface and the dissemination of the pathogen in host tissues (blood, heart, and spleen).

RESULTS

Most of the commensal bacteria present in the skin of control mice were replaced during the blood-feeding process by bacteria originating from the ticks. The microbiome of the ticks was also impacted by the blood feeding. Several pathogens including tick-borne pathogens (Borrelia/Borreliella, Anaplasma, Neoehrlichia, Rickettsia) and opportunistic bacteria (Williamsia) were transmitted to the skin microbiome and some of them disseminated to the blood or spleen of the mice. In the different experiments of this study, skin microbiome alteration and Borrelia/Borreliella transmission were different depending on the tick stages (nymphs or adult female ticks).

CONCLUSIONS

Host skin microbiome at the bite site was deeply impacted by the tick bite, to an extent which suggests a role in the tick feeding, in the pathogen transmission, and a potentially important impact on the skin physiopathology. The diversified taxonomic profiles of the tick microbiome were also modified by the blood feeding. Video Abstract.

Microbiomes in agricultural and mining soils contaminated with arsenic in Guanajuato, Mexico

In this report, physical and chemical properties, and total arsenic (As) concentrations were analyzed in agricultural (MASE) and mining soils (SMI) in the State of Guanajuato, México. Additionally, a metagenomic analysis of both types of soils was the bases for the identification and selection of bacteria and fungi resistant to As. The SMI soil showed higher concentration of As (39 mg kg^-1) as compared to MASE soil (15 mg kg^-1). The metagenome showed a total of 175,240 reads from both soils. MASE soil showed higher diversity of bacteria, while the SMI soil showed higher diversity of fungi. 16S rRNA analysis showed that the phylum Proteobacteria showed the highest proportion (39.6% in MASE and 36.4% in SMI) and Acidobacteria was the second most representative (24.2% in SMI and 11.6% in MASE). 18S rRNA analysis, showed that the phylum Glomeromycota was found only in the SMI soils (11.6%), while Ascomycota was the most abundant, followed by Basidiomycota, and Zygomycota, in both soils. Genera Bacillus and Penicillium were able to grow in As concentrations as high as 5 and 10 mM, reduced As (V) to As (III), and removed As at 9.8% and 12.1% rates, respectively. When aoxB, arsB, ACR3(1), ACR3(2,) and arrA genes were explored, only the arsB gene was identified in Bacillus sp., B. simplex, and B. megaterium. In general, SMI soils showed more microorganisms resistant to As than MASE soils. Bacteria and fungi selected in this work may show potential to be used as bioremediation agents in As contaminated soils.

Detection of Nocardia, Streptomyces and Rhodococcus from bronchoalveolar lavage specimens of patients with HIV by Multiplex PCR Assay

Background

Nocardia, Streptomyces and Rhodococcus are life threatening opportunistic pathogens under immunodeficiency conditions, particularly among patients infected with HIV. Rapid and accurate detection of these infections can improve immune health quality, patient management and appropriate treatment. The aim of this study was to design a novel multiplex-PCR assay for rapid diagnosis of these three organisms directly from bronchoalveolar lavage (BAL) specimens of patients infected with HIV.

Methods

The genus specific primers were designed for direct-detection of Nocardia, Streptomyces and Rhodococcus in a single tube multiplex PCR. This PCR specifically amplified the target genes from pure cultures. It subsequently was applied on BAL specimens of 29 HIV positive patients that had previously been culture negative for actinomycete bacteria, of which Nocardia, Streptomyces and Rhodococcus are members.

Results

Of 29 respiratory clinical specimens, there were positive for Nocardia spp. and one was positive for Streptomyces spp using the multiplex PCR assay. The sequencing of the PCR products identified the species as Nocardia cyriacigeorgica (n=2), Nocardia farcinica and Streptomyces albus.

Conclusion

This novel multiplex PCR assay yielded reliable results for accurate identification of Nocardia, Streptomyces and Rhodococcus from BAL while the results of bacterial culture were negative.

Artificial-turf surfaces for sport and recreational activities: microbiota analysis and 16S sequencing signature of synthetic vs natural soccer fields

Synthetic fibres are used in place of the natural grass worldwide, for realizing playgrounds, soccer fields and even domestic gardens or recreational structures. An intensive use of artificial turf is currently observed in sports facilities, due to lower costs, higher sustainability in recycling of materials, and advantages related to athletic practice and performance. However, even if chemical and physical risks were studied, the microbiological component was not fully addressed, especially considering a comprehensive evaluation of the microbiota in synthetic vs natural playground surfaces. Here, we investigated the microbial community present on soccer fields, using Next Generation Sequencing and a 16S amplicon sequencing approach. Artificial and natural turfs show own ecosystems with different microbial profiles and a mean Shannon's diversity value of 2.176 and 2.475, respectively. The bacterial community is significantly different between facilities (ANOSIM: R = 0.179; p < 0.001) and surface materials (ANOSIM: R = 0.172; p < 0.005). The relative abundance of potentially pathogenic bacterial OTUs was higher in synthetic than in natural samples (ANOVA, F = 2.2). Soccer fields are characterized by their own microbiota, showing a different 16S amplicon sequencing signature between natural and artificial turfs.

Technologies for the Selection, Culture and Metabolic Profiling of Unique Rhizosphere Microorganisms for Natural Product Discovery

Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel "rhizochip" prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.

The Cytokinin Complex Associated With Rhodococcus fascians: Which Compounds Are Critical for Virulence?

Virulent strains of Rhodococcus fascians cause a range of disease symptoms, many of which can be mimicked by application of cytokinin. Both virulent and avirulent strains produce a complex of cytokinins, most of which can be derived from tRNA degradation. To test the three current hypotheses regarding the involvement of cytokinins as virulence determinants, we used PCR to detect specific genes, previously associated with a linear virulence plasmid, including two methyl transferase genes (mt1 and mt2) and fas4 (dimethyl transferase), of multiple strains of R. fascians. We inoculated Pisum sativum (pea) seeds with virulent and avirulent strains of R. fascians, monitored the plants over time and compared these to mock-inoculated controls. We used RT-qPCR to monitor the expression of mt1, mt2, and fas4 in inoculated tissues and LC-MS/MS to obtain a comprehensive picture of the cytokinin complement of inoculated cotyledons, roots and shoots over time. The presence and expression of mt1 and mt2 was associated with those strains of R. fascians classed as virulent, and not those classed as avirulent. Expression of mt1, mt2, and fas4 peaked at 9 days post-inoculation (dpi) in cotyledons and at 15 dpi in shoots and roots developed from seeds inoculated with virulent strain 602. Pea plants inoculated with virulent and avirulent strains of R. fascians both contained cytokinins likely to have been derived from tRNA turnover including the 2-methylthio cytokinins and cis-zeatin-derivatives. Along with the isopentenyladenine-type cytokinins, the levels of these compounds did not correlate with virulence. Only the novel 1- and 2-methylated isopentenyladenine cytokinins were uniquely associated with infection by the virulent strains and are, therefore, the likely causative factors of the disease symptoms.