Landscape of global urban environmental resistome and its association with local socioeconomic and medical status.

Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

Development of a genetic tool for functional screening of anti-malarial bioactive extracts in metagenomic libraries.

BACKGROUND: The chemical treatment of Plasmodium falciparum for human infections is losing efficacy each year due to the rise of resistance. One possible strategy to find novel anti-malarial drugs is to access the largest reservoir of genomic biodiversity source on earth present in metagenomes of environmental microbial communities. METHODS: A bioluminescent P. falciparum parasite was used to quickly detect shifts in viability of microcultures grown in 96-well plates. A synthetic gene encoding the Dermaseptin 4 peptide was designed and cloned under tight transcriptional control in a large metagenomic insert context (30 kb) to serve as proof-of-principle for the screening platform. RESULTS: Decrease in parasite viability consistently correlated with bioluminescence emitted from parasite microcultures, after their exposure to bacterial extracts containing a plasmid or fosmid engineered to encode the Dermaseptin 4 anti-malarial peptide. CONCLUSIONS: Here, a new technical platform to access the anti-malarial potential in microbial environmental metagenomes has been developed.

Klebsiella pneumoniae yfiRNB operon affects biofilm formation, polysaccharide production and drug susceptibility.

Klebsiella pneumoniae is an opportunistic pathogen important in hospital-acquired infections, which are complicated by the rise of drug-resistant strains and the capacity of cells to adhere to surfaces and form biofilms. In this work, we carried out an analysis of the genes in the K. pneumoniae yfiRNB operon, previously implicated in biofilm formation. The results indicated that in addition to the previously reported effect on type 3 fimbriae expression, this operon also affected biofilm formation due to changes in cellulose as part of the extracellular matrix. Deletion of yfiR resulted in enhanced biofilm formation and an altered colony phenotype indicative of cellulose overproduction when grown on solid indicator media. Extraction of polysaccharides and treatment with cellulase were consistent with the presence of cellulose in biofilms. The enhanced cellulose production did not, however, correlate with virulence as assessed using a Caenorhabditis elegans assay. In addition, cells bearing mutations in genes of the yfiRNB operon varied with respect to the WT control in terms of susceptibility to the antibiotics amikacin, ciprofloxacin, imipenem and meropenem. These results indicated that the yfiRNB operon is implicated in the production of exopolysaccharides that alter cell surface characteristics and the capacity to form biofilms--a phenotype that does not necessarily correlate with properties related with survival, such as resistance to antibiotics.

Global adaptation to a lipid environment triggers the dormancy-related phenotype of Mycobacterium tuberculosis.

UNLABELLED: Strong evidence supports the idea that fatty acids rather than carbohydrates are the main energy source of Mycobacterium tuberculosis during infection and latency. Despite that important role, a complete scenario of the bacterium's metabolism when lipids are the main energy source is still lacking. Here we report the development of an in vitro model to analyze adaptation of M. tuberculosis during assimilation of long-chain fatty acids as sole carbon sources. The global lipid transcriptome revealed a shift toward the glyoxylate cycle, the overexpression of main regulators whiB3, dosR, and Rv0081, and the increased expression of several genes related to reductive stress. Our evidence showed that lipid storage seems to be the selected mechanism used by M. tuberculosis to ameliorate the assumed damage of reductive stress and that concomitantly the bacilli acquired a slowed-growth and drug-tolerant phenotype, all characteristics previously associated with the dormant stage. Additionally, intergenic regions were also detected, including the unexpected upregulation of tRNAs that suggest a new role for these molecules in the acquisition of a drug-tolerant phenotype by dormant bacilli. Finally, a set of lipid signature genes for the adaptation process was also identified. This in vitro model represents a suitable condition to illustrate the participation of reductive stress in drugs' activity against dormant bacilli, an aspect scarcely investigated to date. This approach provides a new perspective to the understanding of latent infection and suggests the participation of previously undetected molecules. IMPORTANCE: Mycobacterium tuberculosis establishes long-lasting highly prevalent infection inside the human body, called latent tuberculosis. The known involvement of fatty acids is changing our understanding of that silent infection; however, question of how tubercle bacilli globally adapt to a lipid-enriched environment is still an unanswered. With the single change of providing fatty acids as carbon sources, the bacilli switch on their program related to dormant stage: slowed growth, accumulation of lipid bodies, and development of drug tolerance. In this stage, unexpected and previously unknown participants were found to play putatively important roles during the process. For the first time, this work compares the global transcriptomics of bacteria by using strand-specific RNA sequencing under two different growth conditions. This study suggests novel targets for the control of tuberculosis and provides a new straightforward in vitro model that could help to test the activity of drugs against dormant bacilli from a novel perspective.

Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities.

Microbial explorations of hot springs have led to remarkable discoveries and improved our understanding of life under extreme conditions. The Andean Mountains harbor diverse habitats, including an extensive chain of geothermal heated water sources. In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. The diversity and structure of the microbial communities were assessed by pyrosequencing the V5 - V6 region of the 16S rRNA gene. The planktonic communities varied in terms of diversity indexes and were dominated by the bacterial phyla Proteobacteria, Aquificae, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, and Thermotogae, with site-specific bacterial taxa also observed in some cases. Statistical analyses showed that these microbial communities were distinct from one another and that they clustered in a manner consistent with physicochemical parameters of the environment sampled. Multivariate analysis suggested that pH and sulfate were among the main variables influencing population structure and diversity. The results show that despite their geographical proximity and some shared geochemical characteristics, there were few shared operational taxonomic units (OTUs) and that community structure was influenced mainly by environmental factors that have resulted in different microbial populations.

Exploration of noncoding sequences in metagenomes.

Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C) content, Codon Usage (Cd), Trinucleotide Usage (Tn), and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS) in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

Distribución de bacterias potencialmente fijadoras de nitrógeno y su relación con parámetros fisicoquímicos en suelos con tres coberturas vegetales en el sur de la Amazonia colombiana

Distribution of potentially nitrogen-fixing bacteria and its relationship with physicochemical parameters in soils with three vegetation types in the southern Colombian Amazon region. Potentially nitrogen-fixing microaerobic and aerobic bacteria were isolated from several Colombian Amazon soils (forest, pastures and chagras) and two landscapes (floodable and non floodable areas). The abundance and distribution of bacteria were evaluated, as well as their relationship with soil physical and chemical characteristics. Landscape had a direct influence on the abundance of the microaerobic bacteria, with higher numbers in forest and pasture soils in non- floodable zones. The aerobic isolates (N=51) were grouped into 19 morphologies, with the highest numbers found in forest soil in floodable zones. A higher number of aerobic morphologies was shared among forest sites (Nonmetric Multidimensional Scaling and Analysis of Similarity p<0.05), and 40% of the distribution was explained by lime percentage and Al concentration. Rev. Biol. Trop. 57 (4): 915- 927. Epub 2009 December 01.

Se evaluó la abundancia y distribución de bacterias microaerófilas y aerobias potencialmente fijadoras de nitrógeno aisladas a partir de suelos bajo coberturas de bosque, pastizal y chagra en dos paisajes, terraza y llanura inundable, en el sur de trapecio amazónico. Se relacionó el recuento en placa en el medio Ashby de estas bacterias aerobias con las características físicas y químicas del suelo. Se encontró mayor abundancia de bacterias aerobias y microaerofilas en suelos bajo cobertura de pastizal. Se observó influencia directa del paisaje sobre la abundancia de bacterias microaerófilas registrando mayores recuentos los suelos bajo terraza en las coberturas de bosque y pastizal. Los aislamientos aerobios obtenidos (51) se agruparon en 19 morfologías, de las cuales se obtuvo mayor número en suelos bajo bosque y en el paisaje de llanura inundable. A través del análisis multidimensional no métrico (NMDS) y análisis de similaridades (ANOSIM) (p<0.05) se comprobó que entre los sitios de muestreo bajo la cobertura de bosque se comparten mayor número de morfologías de bacterias aerobias que bajo las demás coberturas. El programa BIOENV indicó que esta distribución fue explicada en un 40% por las variables % limo y Al (meq/100 g).

[Distribution of potentially nitrogen-fixing bacteria and its relationship with physicochemical parameters in soils with three vegetation types in the southern Colombian Amazon region]. / Distribución de bacterias potencialmente fijadoras de nitrógeno y su relación con parámetros fisicoquímicos en suelos con tres coberturas vegetales en el sur de la Amazonia colombiana.

Potentially nitrogen-fixing microaerobic and aerobic bacteria were isolated from several Colombian Amazon soils (forest, pastures and chagras) and two landscapes (floodable and non floodable areas). The abundance and distribution of bacteria were evaluated, as well as their relationship with soil physical and chemical characteristics. Landscape had a direct influence on the abundance of the microaerobic bacteria, with higher numbers in forest and pasture soils in non-floodable zones. The aerobic isolates (N=51) were grouped into 19 morphologies, with the highest numbers found in forest soil in floodable zones. A higher number of aerobic morphologies was shared among forest sites (Nonmetric Multidimensional Scaling and Analysis of Similarity p<0.05), and 40% of the distribution was explained by lime percentage and Al concentration.