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Aquaculture is an important component of the world food supply and a significant source of protein. However, this industry faces numerous problems. Including poor fish feed digestion and uneconomic nutrient utilization. This can result in unsatisfactory growth rates and poor stock performance. Utilizing probiotics, which are beneficial microbes that can enhance digestive systems and general fish health, is one possible way to address these issues. This study was designed to identify and evaluate a novel strain of Bacillus as a promising probiotic. The strain of Bacillus rugosus that was examined and coded NM007 showed promising probiotic characteristics that could help fish digest and utilize their feed more efficiently, reduce feed waste, and improve their digestive systems. B. rugosus NM007 exhibited the ability to produce digestive enzymes like protease, amylase, and lipase, which are the main digestive enzymes. It showed strong auto-aggregation activity and co-aggregation activity with Aeromonas sp. and Streptococcus sp. It also demonstrated tolerance to the presence of bile salt, acidic pH, and salinity up to 60 ppt. The sensitivity analysis towards antibiotics, hemolytic activity and the safety assessment on Nile tilapia fish (Oreochromis niloticus) confirmed the safety of this isolate. Based on the findings of this investigation and the isolate's characterization, Bacillus rugosus NM007 could serve as a new promising probiotic bacterium for aquaculture., (© 2024. The Author(s).)

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., (© 2024. Science China Press.)

Hospital environmental surfaces are potential reservoirs for transmitting hospital-associated pathogens. This study aimed to profile microbiomes and antibiotic resistance genes (ARGs) from hospital environmental surfaces using 16S rRNA amplicon and metagenomic sequencing at a tertiary teaching hospital in Malaysia. Samples were collected from patient sinks and healthcare staff counters at surgery and orthopaedic wards. The samples' DNA were subjected to 16S rRNA amplicon and shotgun sequencing to identify bacterial taxonomic profiles, antibiotic resistance genes, and virulence factor pathways. The bacterial richness was more diverse in the samples collected from patient sinks than those collected from staff counters. Proteobacteria and Verrucomicrobia dominated at the phylum level, while Bacillus , Staphylococcus , Pseudomonas , and Acinetobacter dominated at the genus level. Staphylococcus epidermidis and Staphylococcus aureus were prevalent on sinks while Bacillus cereus dominated the counter samples. The highest counts of ARGs to beta-lactam were detected, followed by ARGs against fosfomycin and cephalosporin. We report the detection of mcr-10.1 that confers resistance to colistin at a hospital setting in Malaysia. The virulence gene pathways that aid in antibiotic resistance gene transfer between bacteria were identified. Environmental surfaces serve as potential reservoirs for nosocomial infections and require mitigation strategies to control the spread of antibiotic resistance bacteria.

The Johor Strait separates the island of Singapore from Peninsular Malaysia. A 1-kilometer causeway built in the early 1920s in the middle of the strait effectively blocks water flowing to/from either side, resulting in low water turnover rates and build-up of nutrients in the inner Strait. We have previously shown that short-term rather than seasonal environmental changes influence microbial community composition in the Johor Strait. Here, we present a temporally-intensive study that uncovers the factors keeping the microbial populations in check. We sampled the surface water at four sites in the inner Eastern Johor Strait every other day for two months, while measuring various water quality parameters, and analysed 16S amplicon sequences and flow-cytometric counts. We discovered that microbial community succession revolves around a common stable state resulting from frequent pulse disturbances. Among these, sporadic riverine freshwater input and regular tidal currents influence bottom-up controls including the availability of the limiting nutrient nitrogen and its biological release in readily available forms. From the top-down, marine viruses and predatory bacteria limit the proliferation of microbes in the water. Harmful algal blooms, which have been observed historically in these waters, may occur only when there are simultaneous gaps in the top-down and bottom-up controls. This study gains insight into complex interactions between multiple factors contributing to a low-resistance but high-resilience microbial community and speculate about rare events that could lead to the occurrence of an algal bloom., (© 2023. The Author(s).)

In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment., (Copyright © 2021. Published by Elsevier Inc.)

Direct analysis of the colonised surface on coal using attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) revealed the nature of bacteria-mediated oxidation at the coal surface. Unique oxidation peaks generated by the presence of Pseudomonas fluorescens on coal was shown through ATR-FTIR measurements, and ATR-FTIR imaging illustrated that this peak was only observed within the region of coal colonised by bacteria. Contact angle measurements and surface free energy of adhesion calculations showed that the adhesion between P. fluorescens and coal was thermodynamically favourable, and scanning electron microscopy (SEM) exhibited individual cell or monolayer cluster attachment on coal. Furthermore, Gaussian peak fitting of peroxidase-treated coal ATR-FTIR spectra revealed that peroxidase or related enzymes produced by P. fluorescens may be responsible for coal oxidation. This study demonstrated the usefulness and practicality of ATR-FTIR for analysing coal oxidation by P. fluorescens and may well be applied to other microbe-driven modifications of coal for its rapidity and reliability.

The use of hexamethyldisilazane (HMDS) as a drying agent was investigated in the specimen preparation for scanning electron microscopy (SEM) imaging of bacterial surface colonization on sub-bituminous coal. The ability of microbes to biofragment, ferment and generate methane from coal has sparked interest in the initial attachment and colonization of coal surfaces. HMDS represents an attractive alternative to critical point drying (CPD) in the imaging of cells on coal, negating the need for expensive equipment. Coal is easily fragmented into sub-micron particles, which can be problematic in critical point drying procedures. In this study, both individual and aggregated cells appeared well shaped with minimal occurrence of flattened cells, signifying the suitability of HMDS in cell attachment studies on sub-bituminous coal. In the absence of glucose, microcolonies of short and long cells showed similar positive results using this method. EPS shrinkage found in microcolonies was inevitable, though this enabled observation of points of attachment between cells and with coal, which would be less effective if the EPS was intact. Overall the use of HMDS drying is preferred over the more commonly used CPD method as it is safer, cheaper and more practical., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Nonylphenols (NP) have estrogenic potential because of their phenolic ring, but the organisms involved in the degradation of this alkylated phenol remain unidentified. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP) and a new method based on pyrosequencing, we identified the bacteria involved in the degradation of the aromatic ring of [U-ring-(13)C] 4-n-NP in aerobic sludge. The first order degradation rate of 4-n-NP was 5.5d(-1). Single strand conformation polymorphism of density-separated labeled and unlabeled 16S rRNA showed significant differences and enabled selection of four representative fractions for pyrosequencing. Nineteen phylotypes showed a significant enrichment in the heavy fraction in the labeled pulse. The relative abundances of these phylotypes were combined with the RNA concentration of each fraction to yield a simple model of the distribution of each phylotype across the gradient. This model was used to estimate the percentage of labeling for each phylotype. The sequences showing the highest labeling (11%) were closely related to Afipia sp. but represented only 2 % of the RNA in the heavy fraction of the labeled pulse. The sequences representing the largest proportion of the RNA in the heavy fraction were related to Propionibacterium acnes and Frateuria aurantia, which are known to possess enzymes for phenol degradation. The model shows that despite Afipia having the highest (13)C enrichment, other species encoding phenol degradation pathways are responsible for more (13)C incorporation. Last, we showed that some species represent 12% of the total RNA but contain only 1% (13)C above natural abundance., (Copyright © 2011 Elsevier Ltd. All rights reserved.)