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Bibliography on: Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 08 Nov 2024 at 01:31 Created: 

Metagenomics

While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: ( metagenomic OR metagenomics OR metagenome ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2024-11-07
CmpDate: 2024-11-07

Buytaers FE, Berger N, Van der Heyden J, et al (2024)

The potential of including the microbiome as biomarker in population-based health studies: methods and benefits.

Frontiers in public health, 12:1467121.

The key role of our microbiome in influencing our health status, and its relationship with our environment and lifestyle or health behaviors, have been shown in the last decades. Therefore, the human microbiome has the potential to act as a biomarker or indicator of health or exposure to health risks in the general population, if information on the microbiome can be collected in population-based health surveys or cohorts. It could then be associated with epidemiological participant data such as demographic, clinical or exposure profiles. However, to our knowledge, microbiome sampling has not yet been included as biological evidence of health or exposure to health risks in large population-based studies representative of the general population. In this mini-review, we first highlight some practical considerations for microbiome sampling and analysis that need to be considered in the context of a population study. We then present some examples of topics where the microbiome could be included as biological evidence in population-based health studies for the benefit of public health, and how this could be developed in the future. In doing so, we aim to highlight the benefits of having microbiome data available at the level of the general population, combined with epidemiological data from health surveys, and hence how microbiological data could be used in the future to assess human health. We also stress the challenges that remain to be overcome to allow the use of this microbiome data in order to improve proactive public health policies.

RevDate: 2024-11-07

Wang H, Wang H, Crowther TW, et al (2024)

Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession.

ISME communications, 4(1):ycae128 pii:ycae128.

There is growing awareness of the need for regenerative practices in the fight against biodiversity loss and climate change. Yet, we lack a mechanistic understanding of how microbial community composition and functioning are likely to change alongside transition from high-density tillage to large-scale vegetation restoration. Here, we investigated the functional dynamics of microbial communities following a complete vegetation successional chronosequence in a subtropical zone, Southwestern China, using shotgun metagenomics approaches. The contents of total soil phosphorus (P), available P, litter P, and microbial biomass P decreased significantly during vegetation succession, indicating that P is the most critical limiting nutrient. The abundance of genes related to P-uptake and transport, inorganic P-solubilization, organic P-mineralization, and P-starvation response regulation significantly increased with successional time, indicating an increased microbial "mining" for P under P limitation. Multi-analysis demonstrated microbial P limitation strongly inhibits carbon (C) catabolism potential, resulting in a significant decrease in carbohydrate-active enzyme family gene abundances. Nevertheless, over successional time, microorganisms increased investment in genes involved in degradation-resistant compounds (lignin and its aromatic compounds) to acquire P resources in the litter. Our study provides functional gene-level insights into how P limitation during vegetation succession in subtropical regions inhibits soil microbial C metabolic processes, thereby advancing our understanding of belowground C cycling and microbial metabolic feedback during forest restoration.

RevDate: 2024-11-07

Rizzo C, Dastager SG, H Ay (2024)

Editorial: Microbial biodiversity and bioprospecting in polar ecosystems in the genomics era.

Frontiers in microbiology, 15:1504105.

RevDate: 2024-11-07
CmpDate: 2024-11-07

Devic M, Dennu L, Lozano JC, et al (2024)

An INDEL genomic approach to explore population diversity of phytoplankton.

BMC genomics, 25(1):1045.

BACKGROUND: Although metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. This is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time.

RESULTS: To gain insight into population diversity, a novel method based on INDEL markers was developed on Bathycoccus prasinos (Mamiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. Long read sequencing was first used to characterize structural variants among the genomes of six B. prasinos strains sampled from geographically distinct regions in the world ocean. Markers derived from identified insertions/deletions were validated by PCR then used to genotype 55 B. prasinos strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer (Mediterranean Sea, France). This led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity of B. prasinos. Finally, selected markers were directly tracked on environmental DNA sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics.

CONCLUSIONS: This method, which involves (i) pre-identifying the genetic diversity of B. prasinos in environmental samples by PCR, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative of B. prasinos diversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only in B. prasinos but also potentially in other generalist phytoplankton species.

RevDate: 2024-11-07
CmpDate: 2024-11-07

Beránková T, Arora J, Romero Arias J, et al (2024)

Termites and subsocial roaches inherited many bacterial-borne carbohydrate-active enzymes (CAZymes) from their common ancestor.

Communications biology, 7(1):1449.

Termites digest wood using Carbohydrate-Active Enzymes (CAZymes) produced by gut bacteria with whom they have cospeciated at geological timescales. Whether CAZymes were encoded in the genomes of their ancestor's gut bacteria and transmitted to modern termites or acquired more recently from bacteria not associated with termites is unclear. We used gut metagenomes from 195 termites and one Cryptocercus, the sister group of termites, to investigate the evolution of termite gut bacterial CAZymes. We found 420 termite-specific clusters in 81 bacterial CAZyme gene trees, including 404 clusters showing strong cophylogenetic patterns with termites. Of the 420 clusters, 131 included at least one bacterial CAZyme sequence associated with Cryptocercus or Mastotermes, the sister group of all other termites. Our results suggest many bacterial CAZymes have been encoded in the genomes of termite gut bacteria since termite origin, indicating termites rely upon many bacterial CAZymes endemic to their guts to digest wood.

RevDate: 2024-11-06
CmpDate: 2024-11-07

Gulyás G, Kakuk B, Dörmő Á, et al (2024)

Cross-comparison of gut metagenomic profiling strategies.

Communications biology, 7(1):1445.

The rapid advancements in sequencing technologies and bioinformatics have enabled metagenomic research of complex microbial systems, but reliable results depend on consistent laboratory and bioinformatics approaches. Current efforts to identify best practices often focus on optimizing specific steps, making it challenging to understand the influence of each stage on microbial population analysis and compare data across studies. This study evaluated DNA extraction, library construction methodologies, sequencing platforms, and computational approaches using a dog stool sample, two synthetic microbial community mixtures, and various sequencing data sources. Our work, the most comprehensive evaluation of metagenomic methods to date. We developed a software tool, termed minitax, which provides consistent results across the range of platforms and methodologies. Our findings showed that the Zymo Research Quick-DNA HMW MagBead Kit, Illumina DNA Prep library preparation method, and the minitax bioinformatics tool were the most effective for high-quality microbial diversity analysis. However, the effectiveness of pipelines or method combinations is sample-specific, making it difficult to identify a universally optimal approach. Therefore, employing multiple approaches is crucial for obtaining reliable outcomes in microbial systems.

RevDate: 2024-11-07

Ottinger S, Larson AB, Mercado-Evans V, et al (2024)

Distinct maternofetal immune signatures delineate preterm birth onset following urinary tract infection.

bioRxiv : the preprint server for biology.

Preterm birth is the leading cause of infant mortality resulting in over one million neonatal deaths annually. Maternal urinary tract infection (UTI) during pregnancy increases risk for preterm birth; however, biological processes mediating UTI-associated preterm birth are not well-described. We established a murine maternal UTI model in which challenge with uropathogenic E. coli resulted in preterm birth in about half of dams. Dams experiencing preterm birth displayed excessive bladder inflammation and altered uteroplacental T cell polarization compared to non-laboring infected dams, with no differences in bacterial burdens. Additional factors associated with preterm birth included higher proportions of male fetuses and lower maternal serum IL-10. Furthermore, exogenous maternal IL-10 treatment absolved UTI-associated preterm birth but contributed to fetal growth restriction in this model. Using urine samples from a cohort of human pregnancies with or without UTI, we correlated urinary cytokines with birth outcomes and urine culture status. These analyses yielded a non-invasive, highly predictive three-model system for evaluating preterm birth risk implicating cytokines IL-10, IL-15, IL-1β, and IL-1RA. Our unique bimodal murine model coupled with patient samples provides a platform to investigate immunological and microbial factors governing UTI-associated preterm birth, revealing novel therapeutic opportunities to predict or prevent preterm birth.

RevDate: 2024-11-06
CmpDate: 2024-11-06

Mi J, Jing X, Ma C, et al (2024)

A metagenomic catalogue of the ruminant gut archaeome.

Nature communications, 15(1):9609.

While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.

RevDate: 2024-11-06
CmpDate: 2024-11-06

Xu B, Song P, Jiang F, et al (2024)

Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates.

NPJ biofilms and microbiomes, 10(1):120.

Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.

RevDate: 2024-11-06
CmpDate: 2024-11-06

Bontemps Z, Abrouk D, Venier S, et al (2024)

Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave.

NPJ biofilms and microbiomes, 10(1):121.

Tourism in Paleolithic caves can cause an imbalance in cave microbiota and lead to cave wall alterations, such as dark zones. However, the mechanisms driving dark zone formation remain unclear. Using shotgun metagenomics in Lascaux Cave's Apse and Passage across two years, we tested metabarcoding-derived functional hypotheses regarding microbial diversity and metabolic potential in dark zones vs unmarked surfaces nearby. Taxonomic and functional metagenomic profiles were consistent across years but divergent between cave locations. Aromatic compound degradation genes were prevalent inside and outside dark zones, as expected from past biocide usage. Dark zones exhibited enhanced pigment biosynthesis potential (melanin and carotenoids) and melanin was evidenced chemically, while unmarked surfaces showed genes for antimicrobials production, suggesting that antibiosis might restrict the development of pigmented microorganisms and dark zone extension. Thus, this work revealed key functional microbial traits associated with dark zone formation, which helps understand cave alteration processes under severe anthropization.

RevDate: 2024-11-06

Jiang X, Zhang Z, Wu X, et al (2024)

Heterologous Biosynthesis of Betanin Triggers Metabolic Reprogramming in Tobacco.

Metabolic engineering pii:S1096-7176(24)00144-7 [Epub ahead of print].

Engineering of a specialized metabolic pathway in plants is a promising approach to produce high-value bioactive compounds to address the challenges of climate change and population growth. Understanding the interaction between the heterologous pathway and the native metabolic network of the host plant is crucial for optimizing the engineered system and maximizing the yield of the target compound. In this study, we performed transcriptomic, metabolomic and metagenomic analysis of tobacco (Nicotiana tabacum) plants engineered to produce betanin, an alkaloid pigment that is found in Caryophyllaceae plants. Our data reveals that, in a dose-dependent manor, the biosynthesis of betanin promotes carbohydrate metabolism and represses nitrogen metabolism in the leaf, but enhances nitrogen assimilation and metabolism in the root. By supplying nitrate or ammonium, the accumulation of betanin increased by 1.5∼3.8-fold in leaves and roots of the transgenic plants, confirming the pivotal role of nitrogen in betanin production. In addition, the rhizosphere microbial community is reshaped to reduce denitrification and increase respiration and oxidation, assistant to suppress nitrogen loss. Our analysis not only provides a framework for evaluating the pleiotropic effects of an engineered metabolic pathway on the host plant, but also facilitates the development of novel strategies to balance the heterologous process and the native metabolic network for the high-yield and nutrient-efficient production of bioactive compounds in plants.

RevDate: 2024-11-06

Liu Y, Wang Y, Shi W, et al (2024)

Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome.

The Science of the total environment pii:S0048-9697(24)07539-9 [Epub ahead of print].

Bacteriophages ("phage") play important roles in nutrient cycling and ecology in environments by regulating soil microbial community structure. Here, metagenomic sequencing showed that a low relative abundance of nitrogen-fixing bacteria but high abundance of Enterobacter-infecting phages in paddy soil where rice plants showed nitrogen deficiency. From soil in the same field, we also isolated and identified a novel virulent phage (named here as Apdecimavirus NJ2) that infects several species of Enterobacter and characterized its impact on nitrogen fixation in the soil and in plants. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on genomic characteristics, comparative genomics and phylogenetic analysis, Apdecimavirus NJ2 should be a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Controlling phages in the soil could be a useful strategy for improving soil nitrogen fixation.

RevDate: 2024-11-06

Zheng B, Zhou L, Wang J, et al (2024)

The shifts in microbial interactions and gene expression caused by temperature and nutrient loading influence Raphidiopsis raciborskii blooms.

Water research, 268(Pt B):122725 pii:S0043-1354(24)01624-5 [Epub ahead of print].

Climate change and the trophic status of water bodies are important factors in global occurrence of cyanobacterial blooms. The aim of this study was to explore the cyanobacteria‒bacterial interactions that occur during Raphidiopsis raciborskii (R. raciborskii) blooms by conducting microcosm simulation experiments at different temperatures (20 °C and 30 °C) and with different phosphorus concentrations (0.01 mg/L and 1 mg/L) using an ecological model of microbial behavior and by analyzing microbial self-regulatory strategies using weighted gene coexpression network analysis (WGCNA). Three-way ANOVA revealed significant effects of temperature and phosphorus on the growth of R. raciborskii (P < 0.001). The results of a metagenomics-based analysis of bacterioplankton revealed that the synergistic effects of both climate and trophic changes increased the ability of R. raciborskii to compete with other cyanobacteria for dominance in the cyanobacterial community. The antagonistic effects of climate and nutrient changes favored the occurrence of R. raciborskii blooms, especially in eutrophic waters at approximately 20 °C. The species diversity and richness indices differed between the eutrophication treatment group at 20 °C and the other treatment groups. The symbiotic bacterioplankton network revealed the complexity and stability of the symbiotic bacterioplankton network during blooms and identified the roles of key species in the network. The study also revealed a complex pattern of interactions between cyanobacteria and non-cyanobacteria dominated by altruism, as well as the effects of different behavioral patterns on R. raciborskii bloom occurrence. Furthermore, this study revealed self-regulatory strategies that are used by microbes in response to the dual pressures of temperature and nutrient loading. These results provide important insights into the adaptation of microbial communities in freshwater ecosystems to environmental change and provide useful theoretical support for aquatic environmental management and ecological restoration efforts.

RevDate: 2024-11-06

Li ZT, HP Zhao (2024)

Sulfate-driven microbial collaboration for synergistic remediation of chloroethene-heavy metal pollution.

Water research, 268(Pt B):122738 pii:S0043-1354(24)01637-3 [Epub ahead of print].

The treatment of heavy metal(loid) (HM) composite pollution has long posed a challenge for the bioremediation of organohalide-contaminated sites. Given the prevalent cohabitation of sulfate-reducing bacteria (SRB) with organohalide-respiring bacteria (OHRB), we proposed a sulfate-amendment strategy to achieve synergistic remediation of trichloroethene and diverse HMs [50μM of As(III), Ni(II), Cu(II), Pb(II)]. Correspondingly, 50-75 μM sulfate was introduced to HM inhibitory batches to investigate the enhancement effect of sulfate amendment on bio-dechlorination. Dechlorination kinetics and MATLAB modeling indicated that sulfate amendment comprehensively improved the reductive dechlorination performance in the presence of As(III), Ni(II), Pb(II) and mixed HMs, while no enhancement was observed under Cu(II) exposure. Additionally, sulfate introduction effectively accelerated the detoxification of Ni(II), Pb(II), Cu(II), and As(III), achieving removal efficiencies of 76.87 %, 64.01 %, 86.37 %, and 95.50 % within the first three days, respectively. Meanwhile, propionate dynamics and acetogenesis indicated enhanced carbon source and e-donor supply. 16S rRNA gene sequencing and metagenomic analysis results demonstrated that HM sequestration was accomplished jointly by SRB and HM-resistant bacteria via extracellular precipitation (metal sulfide) and intracellular sequestration, while their contribution depended on the specific coexisting HM species present. This study highlights the critical role of sulfate in the concurrent bioremediation of HM-organohalide composite contamination and provides insights for developing a cost-effective in-situ bioremediation strategy.

RevDate: 2024-11-06

Jiang K, Yang X, Gao Q, et al (2024)

Exogenous signaling molecules N-acyl-homoserine lactones promotes the reconstruction of sludge particles after impact with highly concentrated urea-formaldehyde resin microplastics.

Journal of environmental management, 371:123179 pii:S0301-4797(24)03165-7 [Epub ahead of print].

In this study, exogenous N-acyl-homoserine lactones (AHLs) was added to resist the stress by high concentration (0.5 g/L) of urea formaldehyde resin microplastics (UF-MPs) on anaerobic granular sludge (AnGS), aiming to provide a viable strategy for AnGS to withstand elevated levels of UF-MPs toxicity elucidate the intricate regulatory mechanism of AHL-mediated AnGS-QS regulation. The results showed that the three different signaling molecules (C4-HSL, C6-HSL, and C8-HSL) improved the performance of AnGS under high concentration (0.5 g/L) urea-formaldehyde resin stress, and increased sludge COD removal (4.48%, 4.76%, and 3.35%, respectively) and methanogenic activity (8.38%, 1.92%, and 18.76%, respectively). The addition of C4-HSL has the best effect on sludge particle size and strength, which is attributed to the fact that C4-HSL can significantly increase the content of polysaccharides and proteins in tightly bound extracellular polymeric substances (TB-EPS) (27.1% and 27.1%, respectively). C8-HSL most obviously promotes energy metabolism and EPS biosynthesis gene expression. Metagenomic analysis showed that trace AHLs could promote the abundance of enzymes and functional genes related to the main pathway of methane metabolism, increase the relative abundance of Methanothrix of acetophilic methanogens from 27.79% in the control group to 27.85% (C4-HSL), 28.90% (64-HSL), and 30.03% (C8-HSL), thereby improving community stability.

RevDate: 2024-11-06
CmpDate: 2024-11-06

Qin X, Cheng J, Qiu Y, et al (2024)

Characterization of psychrotrophic and thermoduric bacteria in raw milk using a multi-omics approach.

Microbial genomics, 10(11):.

Psychrotrophic and thermoduric bacteria are the main reasons for the spoilage of dairy products. This study aims to address the composition and function of psychrotrophic and thermoduric bacteria in eight groups of raw milk samples obtained from Heilongjiang Province and Inner Mongolia (China). Microbial enumeration showed an average total bacterial count of 4.63 log c.f.u. ml[-1] and psychrotrophic bacterial counts of 4.82 log c.f.u. ml[-1]. The mean counts of mesophilic and thermophilic thermoduric bacteria were 3.68 log and 1.81 log c.f.u. ml[-1], respectively. Isolated psychrotrophic bacteria (26 genera and 50 species) and mesophilic thermoduric bacteria (20 genera and 32 species) showed high microbial diversity. Through metagenomic and proteomic analyses, significant disparities in the concentration and community structure of psychrotrophic and thermoduric bacteria were observed among different locations. A large number of peptidases were annotated by metagenomics, which may result in milk spoilage. They mainly come from some typical psychrotrophic and thermoduric bacteria, such as Chryseobacterium, Epilithonimonas, Pseudomonas, Psychrobacter, Acinetobacter, Lactococcus, Escherichia and Bacillus. However, the main proteins detected in fresh raw milk were associated with bacterial growth, reproduction and adaptation to cold environments. This investigation provides valuable insights into the microbial communities and protein profiles of raw milk, shedding light on the microbial factors contributing to milk deterioration.

RevDate: 2024-11-06

Xiao W, Weissman JL, PLF Johnson (2024)

Ecological drivers of CRISPR immune systems.

mSystems [Epub ahead of print].

UNLABELLED: CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR systems. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity.

IMPORTANCE: Microbes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.

RevDate: 2024-11-06

Li M, Thieringer PH, Bayer B, et al (2024)

Genome sequence of Nitrosopumilus adriaticus CCS1 assembled from an ammonia-oxidizing enrichment culture.

Microbiology resource announcements [Epub ahead of print].

We report the metagenome-assembled genome of an ammonia-oxidizing archaeon that is closely related to Nitrosopumilus adriaticus NF5 but shows distinct genomic features compared to strain NF5.

RevDate: 2024-11-06

Sun H, Liu X, Wang T, et al (2024)

Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.

Applied and environmental microbiology [Epub ahead of print].

UNLABELLED: Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.

IMPORTANCE: Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.

RevDate: 2024-11-06

Wasserman MG, Greenberg J, Hall B, et al (2024)

Plasma Microbial Cell-Free DNA Metagenomic Next-Generation Sequencing in People With Cystic Fibrosis.

RevDate: 2024-11-06

Wu Y, You Y, Wu L, et al (2024)

Integrated metagenomics and metatranscriptomics analyses reveal the impacts of different Lactiplantibacillus plantarum strains on microbial communities and metabolic profiles in pickled bamboo shoots.

Food chemistry, 464(Pt 2):141772 pii:S0308-8146(24)03422-8 [Epub ahead of print].

Effects of two different Lactobacillus plantarum fermentation processes on microbial communities and metabolic functions were evaluated using metagenomics and metatranscriptomics. Dominant species in Lactobacillus plantarum DACN4208 (LPIF8) and DACN4120 (LPIF10) were Lactobacillus pentosus and Lactobacillus plantarum, with Lactiplantibacillus comprised 75.31 % of the microbial community in LPIF10. Metatranscriptomic revealed that LPIF8 had more genes associated with carbohydrate-binding modules and auxiliary activities, totaling 7500 and 4000 genes, respectively. Metabolic reconstruction further showed that LPIF8 had the most genes involved in pyruvate and lactose metabolism, with 633 and 389 genes, respectively. In contrast, LPIF10 fewer genes related to the biosynthesis and metabolism of phenylalanine, tyrosine, and tryptophan. These results indicate that LPIF8 could efficiently improve fermentation efficiency and increase metabolic activity, while LPIF10 exhibited a more moderate and controlled metabolic process. These provide valuable insights into how different starter cultures influence the structure and metabolic functions of microbial communities in pickled bamboo shoots.

RevDate: 2024-11-06

Kerek A, Szabó E, Szabó Á, et al (2024)

Investigating antimicrobial resistance genes in probiotic products for companion animals.

Frontiers in veterinary science, 11:1464351.

INTRODUCTION: One of the greatest challenges of our time is antimicrobial resistance, which could become the leading cause of death globally within a few decades. In the context of One Health, it is in the common interest to mitigate the global spread of antimicrobial resistance by seeking alternative solutions, alongside appropriate drug selection and responsible use. Probiotics offer a potential avenue to reduce antibiotic usage; however, there is a scarcity of research that examines commercial products in terms of carrying antimicrobial resistance genes (ARGs) involved in resistance development through microbial vectors.

METHODS: Our study investigated 10 commercially available probiotic products for cats and dogs. Initially, we conducted phenotypic testing through determination of minimum inhibitory concentration (MIC) for antibiotics important in animal and public health. Subsequently, we performed next-generation sequencing (NGS) of the products to elucidate the genetic background behind the decrease in phenotypic sensitivity.

RESULTS: In total, 19 types of ARGs were identified, with 57.9% being found on plasmids, and in two cases, carriage as mobile genetic elements were found. One of the genes identified was the APH(3')-Ia gene, capable of inactivating aminoglycoside antibiotics through phosphotransferase enzyme production regulation, while the other was the tetS gene, capable of conferring reduced sensitivity to tetracycline antibiotics through target protection.

DISCUSSION: Our findings underscore the importance of approaching antimicrobial resistance investigations from a broader perspective. We suggest that further studies in this area are justified and raise questions regarding the need to extend legally required studies on probiotic products from their use in economic livestock to their use in companion animals.

RevDate: 2024-11-06

Knight R, Guccione C, Patel L, et al (2024)

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.

Research square pii:rs.3.rs-4721159.

As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.

RevDate: 2024-11-06

Das R, Tamang B, Najar IN, et al (2024)

Probiotic yeast characterization and fungal amplicon metagenomics analysis of fermented bamboo shoot products from Arunachal Pradesh, northeast India.

Heliyon, 10(20):e39500.

This study investigates the diverse fungal community and their probiotic functions present in ethnic fermented bamboo shoots of Arunachal Pradesh. Among 95 yeast isolates, 13 demonstrated notable probiotic attributes. These included growth at pH 3, bile tolerance, autoaggregation, co-aggregation, hydrophobicity, lysozyme tolerance and antimicrobial activity. Confirmation of some of the probiotic properties through specific primers enabled the detection of genes associated with acid and bile tolerance, antimicrobial activity, and adhesion. Probiotic yeasts were finally identified based on D1 and D2 sequences of large ribosomal subunit as Meyerozyma guilliermondii (BEP1, KGM1_3, NHR3), Meyerozyma caribbica (GEP7), Candida orthopsilopsis (ES1_2, EB1_2, EEGM2_4, GEP2, NEK9), Candida parasilopsis (HD1_1), Pichia kudriavzevii (NHR12), Pichia fermentans (BEP2), and Saccharomyces cerevisiae (NEP2). Fungal amplicon sequencing highlighted the predominance of Ascomycetes, particularly Pestalotiopsis and Penicillium genera. In this study we have perfomed a culture dependent isolation and probiotic study of yeasts and culture independent analysis of the fungal community present during the fermentation of bamboo shoots of Arunachal Pradesh which provides information about the beneficial properties of bamboo shoots as the reservoir of probiotic microorganisms.

RevDate: 2024-11-06

Pilliol V, Mahmoud Abdelwadoud B, Aïcha H, et al (2024)

Methanobrevibacter oralis: a comprehensive review.

Journal of oral microbiology, 16(1):2415734.

Methanobrevibacter oralis (M. oralis) has predominated human oral microbiota methanogenic archaea as far back as the Palaeolithic era in Neanderthal populations and gained dominance from the 18[th] century onwards. M. oralis was initially isolated from dental plaque samples collected from two apparently healthy individuals allowing its first characterization. The culture of M. oralis is fastidious and has been the subject of several studies to improve its laboratory growth. Various PCR methods are used to identify M. oralis, targeting either the 16S rRNA gene or the mcrA gene. However, only one RTQ-PCR system, based on a chaperonin gene, offers specificity, and allows for microbial load quantification. Next-generation sequencing contributed five draft genomes, each approximately 2.08 Mb (±0.052 Mb) with a 27.82 (±0.104) average GC%, and two ancient metagenomic assembled genomes. M. oralis was then detected in various oral cavity sites in healthy individuals and those diagnosed with oral pathologies, notably periodontal diseases, and endodontic infections. Transmission pathways, possibly involving maternal milk and breastfeeding, remain to be clarified. M. oralis was further detected in brain abscesses and respiratory tract samples, bringing its clinical significance into question. This review summarizes the current knowledge about M. oralis, emphasizing its prevalence, associations with dysbiosis and pathologies in oral and extra-oral situations, and symbiotic relationships, with the aim of paving the way for further investigations.

RevDate: 2024-11-06

Lu S, Xie G, Yuan M, et al (2024)

Metagenomic next-generation sequencing in diagnosing perinephric abscess infection caused by Trichomonas vaginalis.

Precision clinical medicine, 7(4):pbae027.

RevDate: 2024-11-06
CmpDate: 2024-11-06

Jia H, Liu Y, T Liu (2024)

Duration of onset, body temperature and C-reactive protein can be used to predict the results of pus culture in children with acute osteomyelitis of long bones.

Italian journal of pediatrics, 50(1):231.

BACKGROUND: With the application of PCR testing and Metagenomic Next-Generation Sequencing(mNGS), the detection rate of causative organisms in paediatric bone and joint infections has been greatly improved. The aim of our study is to identify some indicators that could be used to distinguish the culture results to optimize the use of PCR and mNGS.

METHODS: In this study, a total of 117 cases of acute osteomyelitis of long bones in children who underwent pus culture were included. Patients were grouped as culture-negative (n:21) and culture-positive (n:96) groups according to the results of pus culture. Age, sex, duration of onset, maximum body temperature at onset, inflammatory indicators and D-dimer after admission were systematically collected for all patients and were compared for both groups. ROC curve (ROC) was used to evaluate the diagnostic efficiency of culture-negative. Logistic regression analysis was conducted to determine independent risk factors for culture-negative.

RESULTS: There was no significant difference in age, sex and erythrocyte sedimentation rate between culture-negative group and culture-positive group (P > 0.05). The duration of onset was longer, and the temperature, white blood cells, neutrophils count, C-reactive protein and D-dimer were less elevated in culture-negative acute osteomyelitis (P < 0.05). Duration of onset, maximum body temperature at onset, white blood cell count, neutrophil count, C-reactive protein, and D-dimer have certain diagnostic efficacy in judging the efficacy of negative culture. Logistic regression analysis indicated that the duration of onset more than 6.5 days, the maximum body temperature at onset lower than 38.35℃ and C-reactive protein lower than 78.40 mg/L were independent risk factors for negative culture (P < 0.05).

CONCLUSIONS: Our study revealed that duration of onset more than 6.5 days, maximum body temperature at onset lower than 38.35℃ and C-reactive protein lower than 78.40 mg/L were independent risk factors for predicting negative culture. In children with this type of acute osteomyelitis, we recommend that the pus be tested by PCR or mNGS as a priority.

RevDate: 2024-11-05
CmpDate: 2024-11-06

Deng J, Chen X, Bu Y, et al (2024)

Exploring the appropriate situation of performing CSF mNGS in patients with proposed intracranial infections.

BMC neurology, 24(1):429.

BACKGROUND: Identifying the responsible pathogen is crucial for precision medicine in intracranial infections, and Cerebrospinal Fluid (CSF) Metagenomic Next-Generation Sequencing (mNGS) is a reliable method for this detection. However, the indiscriminate utilization of this approach may impose a financial burden on both patients and society. The study aims to investigate the optimal conditions for applying CSF mNGS in patients with suspected intracranial infections, offering valuable references for precision medicine of intracranial infections.

METHODS: A total of 175 hospitalized patients presenting with suspected intracranial infections were selected for retrospective analysis. Base on the detection of responsible pathogens using CSF mNGS, the patients were categorized into two groups, responsible pathogens in Group A were detected but not in Group B. The types of responsible pathogens in group A and the final diagnosis of patients in group B were analyzed. Demographic data, clinical presentation, CSF analysis, imaging results, and electroencephalography (EEG) findings were analyzed for both groups. Finally, a scoring system was established to promptly assess the appropriateness of CSF mNGS for patients with suspected intracranial infections. Each independent predictor was assigned a score of 1, and the patients were subsequently scored. We advocate sending patients' CSF for mNGS when the cumulative score is ≥ 2.

RESULTS: In Group A, the predominant responsible pathogen was the varicella-zoster virus (VZV), while Group B exhibited the highest proportion of final diagnoses related to epilepsy. The logistic regression model indicates that headache [OR = 2.982, 95% CI (1.204-7.383), p = 0.018], increased cerebrospinal fluid white cell count [OR = 4.022, 95% CI (1.331-12.156), p = 0.014], and decreased cerebrospinal fluid glucose levels [OR = 9.006, 95% CI (2.778-29.194), P < 0.001] are independent predictive factors for intracranial infection pathogens detected by CSF mNGS. Under this scoring system, the sensitivity for detecting the responsible pathogen was 57.5%, and the specificity was 87.4%.

CONCLUSION: The likelihood of detecting the responsible pathogen through CSF mNGS in patients with suspected intracranial infections can be evaluated using the scoring system. Furthermore, it is crucial to consider the possibility of another condition, such as epilepsy, when the responsible pathogen is not detected using cerebrospinal fluid mNGS.

RevDate: 2024-11-05
CmpDate: 2024-11-05

Stewart RD, Oluwalana-Sanusi AE, Munzeiwa WA, et al (2024)

Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa.

Scientific reports, 14(1):26867.

Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.

RevDate: 2024-11-05

Hu X, Bi J, Yu Q, et al (2024)

Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae, Ochotona daurica) in China.

FEMS microbiology letters pii:7876492 [Epub ahead of print].

Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared difference in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (Ochotona daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus and Podoviridae were abundant bacteria, archaea, eukaryotes and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to utilization of pectin, hemicellulose and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk ARGs, such as mepA, tetM and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome, and broadened our understanding of high-risk ARGs and potential pathogens of wild animals.

RevDate: 2024-11-05

Slizovskiy IB, Bonin N, Bravo JE, et al (2024)

Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.

Genome research pii:gr.279226.124 [Epub ahead of print].

We investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining biotinylated probe-based enrichment with long-read sequencing, we facilitated the amplification and sequencing of ARGs, eliminating the need for bioinformatic reconstruction. Our experimental design included replicates of human fecal microbiota transplant material, bovine feces, pristine prairie soil, and a mock human gut microbial community, allowing us to examine variables including genomic DNA input and probe set composition. Our findings demonstrated that TELSeq markedly improves the detection rates of ARGs and MGEs compared to traditional sequencing methods, underlining its potential for accurate AMR monitoring. A key insight from our research is the importance of incorporating mobilome profiles to better predict the transferability of ARGs within microbial communities, prompting a recommendation for the use of combined ARG-MGE probe sets for future studies. We also reveal limitations for ARG detection from low-input workflows, and describe the next steps for ongoing protocol refinement to minimize technical variability and expand utility in clinical and public health settings. This effort is part of our broader commitment to advancing methodologies that address the global challenge of AMR.

RevDate: 2024-11-05

Regar RK, Kamthan M, Gaur VK, et al (2024)

Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis.

Chemosphere pii:S0045-6535(24)02572-4 [Epub ahead of print].

Rivers are critical ecosystems that support biodiversity and local livelihoods. This study aimed to evaluate the effects of metal contamination and anthropogenic activities on microbial and phage community dynamics within major Indian river ecosystems, focusing on the Ganga, Narmada, Cauvery, and Gomti rivers -using metagenomic techniques, Biolog, and ICP-MS analysis. Significant variations in microbial communities were observed both within each river and across the four systems, influenced by ecological factors like geography and hydrology, as well as anthropogenic pressures. Downstream sites consistently exhibited higher microbial diversity, with prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae dominating, while Proteobacteria and Bacteroides declined. The Ganga River showed a higher abundance of bacteriophages compared to other rivers, which gradually reduced with the increment of anthropogenic impact. Functional gene analysis revealed correlations between carbon utilization and metal resistance in contaminated sites. ICP-MS analysis indicates elevated chromium and lead levels in downstream sites of all rivers compared to upstream sites. Interestingly, pristine upstream sites in the Ganga had higher trace element levels than those in Narmada and Cauvery, likely due to its Himalayan origin. Both the Ganga and Cauvery rivers contained numerous metal resistance genes. The Alaknanda was identified as the primary source of microbial communities, bacteriophages, trace elements, and heavy metals in the Ganga. These findings offer new insights into anthropogenic influences on river microbial dynamics and highlight the need for targeted monitoring and management strategies to preserve river health.

RevDate: 2024-11-05

Liu W, Li C, Li B, et al (2024)

Structure-guided discovery and rational design of a new poly(ethylene terephthalate) hydrolase from AlphaFold protein structure database.

Journal of hazardous materials, 480:136389 pii:S0304-3894(24)02968-6 [Epub ahead of print].

Enzymatic degradation offers a promising eco-friendly solution to plastic pollution, especially for polyethylene terephthalate (PET). Current efforts have focused on screening PET-degrading enzymes from microbial and metagenomic sources and obtaining superior candidates with a limited set of templates. More efficient PET hydrolases are required for PET-waste biorefinery. Here, using a structure-guided bioinformatic workflow, we identified a novel PET hydrolase, LSPET4, from Micromonospora sp. HM5-17, by screening the AlphaFold protein structure database. LSPET4 features a unique carbohydrate-binding module (CBM) and a distinctive linear substrate binding conformation. The intrinsic CBM in LSPET4 exhibited superior binding ability on PET surfaces and enhanced PET hydrolysis performance compared to the previously reported most effective CBM3. Through rational protein engineering focused on stabilizing and modifying the linear substrate binding conformation, we developed LSPET4[M6] (D130P, N127F, Y96F, Q209E, A238K, D241S), a variant that achieved a 38.79-fold improvement in activity compared to the wild type, and was comparable to the reported most effective PET hydrolase derived from IsPETase, FAST-PETase at 45 ℃. This variant also demonstrated effectiveness in degrading various commercial PET materials, including PET food sealing films, PET strawberry boxes, and PET tomato boxes used in the food industry. This study not only provides a new template for protein engineering endeavors to create efficient biocatalysts for PET recycling but also offers an effective enzyme discovery approach to uncover enzymes of interest from the AlphaFold protein structure database.

RevDate: 2024-11-05

Adalsteinsson BT, Guðmundsson H, Jasilionis A, et al (2024)

Targeted metagenomics - Enrichment for enzymes active on sulfated polysaccharides from seaweeds.

Enzyme and microbial technology, 182:110528 pii:S0141-0229(24)00135-2 [Epub ahead of print].

Seaweeds (macroalgae) are an attractive resource for diverse microbial- and enzymatic production processes. They are abundant, underutilized, cheap, and rich in carbohydrates, and therefore have the potential to be used as a source of mono- or oligosaccharides, and as substrates for industrial fermentation processes. Many seaweed polysaccharides, including the sulfated polysaccharides ulvan and fucoidan, are however complex and heterogenous in structure, and there are currently few enzymes available to modify them, and understanding of their enzymatic depolymerization remains limited. The present study aimed to identify and characterize robust fucoidanases and ulvan lyases. Metagenomes were obtained from microbial enrichments from an intertidal hot-spring, genes identified that expressed putative fucoidanases and ulvan lyases, and following gene cloning and expression, the respective enzymes were screened for enzymatic activity. Consistent with their origin, the identified protein sequences were considerably divergent from previously characterized enzymes, with a 44 % average maximal sequence identity. In total, the study resulted in the characterization of 10 new fucoidanases (GH107 and GH168 families) and 8 new ulvan lyases (PL24, PL25 and PL40 families). Notably, the new fucoidanases appeared to have functional specificity towards fucoidan containing α-1,3 linked L-fucosyl and several functioned at high temperature. The study contributes a metagenomics-based approach to identify new seaweed polysaccharide degrading enzymes and an increased understanding of the diversity of such enzymes, which may have implications for the realization of biotechnology based valorization of seaweed biomass.

RevDate: 2024-11-05

Zheng X, Xu M, Zhang Z, et al (2024)

Microbial signatures in chronic thromboembolic pulmonary hypertension thrombi: Insights from metagenomic profiling of fresh and organized thrombi.

Thrombosis research, 244:109204 pii:S0049-3848(24)00336-0 [Epub ahead of print].

OBJECTIVE: Many studies have reported microbial signatures in thrombi at major vascular sites, such as the coronary artery and the middle cerebral artery, which are critical for maintaining proper blood flow and oxygenation. Chronic thromboembolic pulmonary hypertension (CTEPH) is a condition involving non-resolving thrombosis that has not been fully studied. This study explored the microbial taxonomy and functional profiles of both fresh and organized thrombi associated with CTEPH to investigate the role of microbiota in thrombus non-resolving.

METHODS: In this study, 12 CTEPH fresh thrombi and 12 organized thrombi were collected from 14 patients with CTEPH. Metagenomic sequencing was employed to explore the genomic information of all microorganisms in the thrombus samples.

RESULTS: Our data demonstrated a diverse range of microorganisms in CTEPH thrombi, whether fresh or organized. Notably, a considerable proportion (54.7 %) of sequencing data could not be classified into the relative microbial taxa, highlighting the complexity and novelty of the thrombus ecosystem. Although there were no significant differences in microbial community structure between the two groups, the abundance of dominant microbial species varied. Leuconostoc sp. DORA 2, Staphylococcus aureus, and Aliidongia dinghuensis were common dominant species in CTEPH thrombus. Organized thrombus significantly increased the relative abundance of Staphylococcus aureus, which was confirmed to effectively distinguish between organized and fresh thrombi by LeFSe analysis and random forest analysis. Functional annotation using both the KEGG and eggNOG databases revealed that organized thrombi exhibit stronger metabolic functions, particularly in amino acid metabolism.

CONCLUSIONS: Our findings suggest that microbial composition and function may play an important role in thrombus organization. Targeting inflammation to prevent thrombosis presents promising opportunities for further research in this area.

RevDate: 2024-11-05
CmpDate: 2024-11-05

Takamiya H, Kouduka M, Kato S, et al (2024)

Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.

The ISME journal, 18(1):.

Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.

RevDate: 2024-11-05

Zhang X, Zhang XX, L Ma (2024)

New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.

Environmental science & technology [Epub ahead of print].

Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.

RevDate: 2024-11-05

Agashe R, George J, Pathak A, et al (2024)

Shotgun metagenomics analysis indicates Bradyrhizobium spp. as the predominant genera for heavy metal resistance and bioremediation in a long-term heavy metal-contaminated ecosystem.

Microbiology resource announcements [Epub ahead of print].

Ten soil cores were collected from the long-term heavy metal-contaminated Savannah River Site (SRS) and studied using shotgun metagenomics. In-line with our previous reports, Bradyrhizobium spp. dominated the SRS soils, and thus we recommend that SRS bioremediation studies target the Bradyrhizobium genus.

RevDate: 2024-11-05

Mukhanbetzhanov N, Jarmukhanov Z, Kozhakhmetov S, et al (2024)

Metagenomic analysis reveals higher Coriobacteriia abundance in mare's milk consumers.

Microbiology resource announcements [Epub ahead of print].

Our study reveals increased gut Coriobacteriia among mare's milk consumers; metagenomic analysis showed a higher prevalence of genera belonging to class Coriobacteriia in consumers vs non-consumers. This suggests interactions between traditional dairy practices and gut microbiome composition, indicating potential for microbiota modulation through dietary interventions.

RevDate: 2024-11-05

Mukherjee S, Stamatis D, Li CT, et al (2024)

Genomes OnLine Database (GOLD) v.10: new features and updates.

Nucleic acids research pii:7875979 [Epub ahead of print].

The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.

RevDate: 2024-11-05

Liang H, Duan X, Li T, et al (2024)

Disseminated Combined Talaromyces marneffei and Enterococcus faecium Bloodstream Infection Presenting as Gastrointestinal Perforation in a Patient with CARD9 Gene Mutation.

Infection and drug resistance, 17:4783-4790.

This study presents a case of Talaromyces marneffei combined with Enterococcus faecium bloodstream infection with gastrointestinal symptoms as the sole initial clinical manifestation.The patient is a resident of Shanghai and has no recent travel history to areas with a high risk of T. marneffei infection. He was admitted to the emergency room due to severe upper abdominal pain. Laboratory tests indicated elevated levels of white blood cells, rapid C-reactive protein, and procalcitonin, while the human immunodeficiency virus (HIV) test returned negative. An abdominal CT examination revealed gas and fluid accumulation in the abdominal cavity, raising suspicion for gastrointestinal perforation and peritonitis. Initially, he received symptomatic treatment for gastrointestinal perforation and abdominal infection, but his response to the treatment was poor.Through metagenomic next-generation sequencing (mNGS) and multiple blood cultures, a mixed infection of T. marneffei and E. faecium was identified in the patient's blood. Combination treatment with vancomycin and amphotericin B was initiated to manage the symptoms. However, we discovered genome-wide exon CARD9 mutations in the patient, complicating the treatment process. Ultimately, the delayed diagnosis of T. marneffei resulted in the patient's severe deterioration, rendering the anti-infective treatment ineffective, and leading to the patient's death.This report underscores the challenges associated with diagnosing T. marneffei infections in non-AIDS patients and in non-endemic regions. The diagnosis of disseminated infections poses significant difficulties, particularly when mixed infections are present, complicating clinical treatment. This highlights the critical importance of standardized blood cultures for the early diagnosis of T. marneffei. Additionally, we must prioritize timely whole-genome testing to identify potential immune gene mutations.

RevDate: 2024-11-05

Barbitoff YA, Khmelkova DN, Pomerantseva EA, et al (2024)

Expanding the Russian allele frequency reference via cross-laboratory data integration: insights from 7452 exome samples.

National science review, 11(10):nwae326.

Population allele frequency is crucially important for accurate interpretation of known and novel variants in medical genetics. Recently, several large allele frequency databases, such as the Genome Aggregation Database (gnomAD), have been created to serve as a global reference for such studies. However, frequencies of many rare alleles vary dramatically between populations, and population-specific allele frequency is often more informative than the global one. Many countries and regions, including Russia, remain poorly studied from the genetic perspective. Here, we report the first successful attempt to integrate genetic information between major medical genetic laboratories in Russia. We construct RUSeq, an open, large-scale reference set of genetic variants by analyzing 7452 exome samples collected in two major Russian cities-Moscow and St. Petersburg. An ∼10-fold increase in sample size compared to previous studies allowed us to characterize extensive genetic diversity within the admixed Russian population with contributions from several major ancestral groups. We highlight 51 known pathogenic variants that are overrepresented in Russia compared to other European countries. We also identify several dozen high-impact variants that are present in healthy donors despite being annotated as pathogenic in ClinVar and falling within genes associated with autosomal dominant disorders. The constructed database of genetic variant frequencies in Russia has been made available to the medical genetics community through a variant browser available at http://ruseq.ru.

RevDate: 2024-11-05

Dias YJM, Dezordi FZ, GDL Wallau (2024)

EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.

Computational and structural biotechnology journal, 23:3662-3668.

Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.

RevDate: 2024-11-05

Maghembe RS, Magulye MAK, Makaranga A, et al (2024)

Metagenome mining divulges virulent and multidrug resistant Pseudomonas aeruginosa ST242 and Klebsiella michiganensis ST∗1b23 coinfecting an 8-month-old meningitis infant under ICU in Kampala, Uganda, East Africa.

Heliyon, 10(20):e39455.

Pediatric meningitis is a global health problem, with insufficiently known pathogens and antibiotic resistance (AMR) especially in low-resource settings. Here, we sought to uncover the virulence and AMR of pathogens associated with infant meningitis, treated with ceftriaxone, in Kampala, Uganda. In a bid to isolate Klebsiella oxytoca, we coincidentally recovered a co-culture and challenged it with antibiotic susceptibility testing (AST) on a panel of 14 antibiotics. We then combined metagenome binning with antiSMASH/PRISM genome mining to unveil the pathogens, their virulence and molecular targets in relation to meningitis. From AST, the co-culture exhibited resistance to multiple aminoglycosides, fluroquinolones, and β-lactams, including ceftriaxone, the inherently used drug. From metagenome annotation, the first bin was identified as Pseudomonas aeruginosa ST242 and the second as Klebsiella michiganensis ST∗1b23. Among others, P. aeruginosa ST242 virulence factors include type 3 and type 6 secretion systems, biofilm, and nonribosomal peptides (NRPs) of the pyoverdine synthase operon, targeting claudin-5, a component of the tight junctions of the blood-brain barrier (BBB). The P. aeruginosa ST242 genome portrays intrinsic resistance to beta-lactamases (blaOXA-50 and blaPAO), aminoglycosides [aph(3')-IIb)], fluoroquinolones (crpP), tetracycline (tmexD2) and fosfomycin (fosA), among others. From K. michiganensis ST∗1b23 genome mining we elucidated a yersiniabactin-related metabolite, targeting the ligand-binding domain of the human polymeric immunoglobulin receptor (pIgR) and other components of the BBB. The K. michiganensis ST∗1b23 chromosome encodes the genes blaOXY-1 and OqxA/B, conferring resistance to β-lactams, fluoroquinolones, and trimethoprim respectively. Notably, we found one frameshift and nine substitution mutations conferring carbapenem and cephalosporin resistance mechanisms. Overall, our findings strongly suggest coinfection and a mechanistic crosstalk between P. aeruginosa ST242 and K. michiganensis ST∗1b23 in the pathogenesis of meningitis in this case. Importantly, ceftriaxone could be an inappropriate treatment choice for these pathogens. Hence, serious surveillance and experimental studies will improve the management of pediatric meningitis.

RevDate: 2024-11-05
CmpDate: 2024-11-05

Li L, Shao J, Tong C, et al (2024)

Non-tuberculous mycobacteria enhance the tryptophan-kynurenine pathway to induce immunosuppression and facilitate pulmonary colonization.

Frontiers in cellular and infection microbiology, 14:1455605.

The increasing prevalence of non-tuberculous mycobacterium (NTM) infections alongside tuberculosis (TB) underscores a pressing public health challenge. Yet, the mechanisms governing their infection within the lung remain poorly understood. Here, we integrate metagenomic sequencing, metabolomic sequencing, machine learning classifiers, SparCC, and MetOrigin methods to profile bronchoalveolar lavage fluid (BALF) samples from NTM/TB patients. Our aim is to unravel the intricate interplay between lung microbial communities and NTM/Mycobacterium tuberculosis infections. Our investigation reveals a discernible reduction in the compositional diversity of the lung microbiota and a diminished degree of mutual interaction concomitant with NTM/TB infections. Notably, NTM patients exhibit a distinct microbial community characterized by marked specialization and notable enrichment of Pseudomonas aeruginosa and Staphylococcus aureus, driving pronounced niche specialization for NTM infection. Simultaneously, these microbial shifts significantly disrupt tryptophan metabolism in NTM infection, leading to an elevation of kynurenine. Mycobacterium intracellulare, Mycobacterium paraintracellulare, Mycobacterium abscessus, and Pseudomonas aeruginosa have been implicated in the metabolic pathways associated with the conversion of indole to tryptophan via tryptophan synthase within NTM patients. Additionally, indoleamine-2,3-dioxygenase converts tryptophan into kynurenine, fostering an immunosuppressive milieu during NTM infection. This strategic modulation supports microbial persistence, enabling evasion from immune surveillance and perpetuating a protracted state of NTM infection. The elucidation of these nuanced microbial and metabolic dynamics provides a profound understanding of the intricate processes underlying NTM and TB infections, offering potential avenues for therapeutic intervention and management.

RevDate: 2024-11-05
CmpDate: 2024-11-05

Steffen KJ, Sorgen AA, Fodor AA, et al (2024)

Early changes in the gut microbiota are associated with weight outcomes over 2 years following metabolic and bariatric surgery.

Obesity (Silver Spring, Md.), 32(11):1985-1997.

OBJECTIVE: Metabolic and bariatric surgery (MBS) is associated with substantial, but variable, weight outcomes. The gut microbiome may be a factor in determining weight trajectory, but examination has been limited by a lack of longitudinal studies with robust microbiome sequencing. This study aimed to describe changes in the microbiome and associations with weight outcomes more than 2 years post surgery.

METHODS: Data were collected at two Midwestern U.S.

CENTERS: Adults undergoing primary MBS were assessed before and 1, 6, 12, 18, and 24 months after surgery. BMI and metagenomic sequencing occurred at each assessment. A linear growth mixture model determined class structure for weight trajectory.

RESULTS: A linear growth mixture model of participants (N = 124) revealed a two-class structure; one class had greater sustained weight loss relative to the other. Greater genus-level taxonomic changes in the microbiome composition at each time point were associated with being in the more favorable weight trajectory class, after controlling for surgery type. Higher Proteobacteria relative abundance at 1 month was predictive of percentage weight change at 6, 12, 18, and 24 months (p < 0.05 for all).

CONCLUSIONS: Greater genus-level taxonomic changes in the gut microbiota are associated with improved weight trajectory. Early changes in the gut microbiota may be an important indicator of MBS outcomes and durability.

RevDate: 2024-11-04
CmpDate: 2024-11-05

Moeller AH, Dillard BA, Goldman SL, et al (2024)

Removal of sequencing adapter contamination improves microbial genome databases.

BMC genomics, 25(1):1033.

Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.

RevDate: 2024-11-04
CmpDate: 2024-11-05

Chen Z, Xiang K, Wang K, et al (2024)

Streptococcus salivarius pneumonia-associated pneumomediastinum: a case report and literature review.

BMC infectious diseases, 24(1):1238.

BACKGROUND: Streptococcus salivarius is an opportunistic pathogen, and there have been no reported cases of Streptococcus salivarius pneumonia to date. Pneumomediastinum is usually secondary to tracheal or esophageal injury and is very rare as a complication of pneumonia. We report a case of Streptococcus salivarius pneumonia complicated by pneumomediastinum, aiming to enhance clinicians' awareness of rare pathogens and uncommon complications in pneumonia.

CASE PRESENTATION: The patient, a 36-year-old male, presented with a persistent cough and sputum production for one week, accompanied by a sore throat that had developed just one day prior. Chest computed tomography (CT) disclosed pneumomediastinum alongside obstructive atelectasis in the left lower lobe. Streptococcus salivarius infection was conclusively identified through bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), as well as smear and culture analyses. The patient was administered intravenous amoxicillin-clavulanate potassium for a duration of seven days as part of the anti-infection regimen. Given the stability of the patient's respiratory and circulatory systems, a tube drainage procedure was deemed unnecessary. Post-treatment, the patient's clinical symptoms notably improved. A subsequent chest CT scan revealed the re-expansion of the left lower lung and near-complete resolution of pneumomediastinum.

CONCLUSION: There are numerous pathogens that can cause pneumonia. While focusing on common pathogens, it is important not to overlook rare ones. When considering infections from rare pathogens, it is recommended to promptly perform a bronchoscopy and submit bronchoalveolar lavage fluid for mNGS to improve pathogen detection rates. During the diagnosis and treatment of pneumonia, it is crucial to be vigilant for rare complications. When a patient presents with symptoms such as dyspnea or subcutaneous emphysema, it is advisable to immediately perform a chest CT scan to rule out pneumomediastinum.

RevDate: 2024-11-05
CmpDate: 2024-11-05

Escuer P, Guirao-Rico S, Arnedo MA, et al (2024)

Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands.

Molecular ecology, 33(22):e17547.

The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage-based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterised genome-wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems.

RevDate: 2024-11-04
CmpDate: 2024-11-04

Payet SD, Underwood J, Berry O, et al (2024)

Population genomics informs the management of harvested snappers across north-western Australia.

Scientific reports, 14(1):26598.

Failure to consider population structure when managing harvested fishes increases the risk of stock depletion, yet empirical estimates of population structure are often lacking for important fishery species. In this study, we characterise genetic variation in single nucleotide polymorphisms (SNPs) to assess population structure for three harvested species of tropical snappers across the broad (up to 300 km wide) and extensive (~ 4000 km) continental shelf of north-western Australia. Comparisons across ~ 300 individuals per species, showed remarkably similar patterns of genetic structure among Lutjanus sebae (red emperor), L. malabaricus (saddletail snapper) and Pristipomoides multidens (goldband snapper) despite subtle differences in biological and ecological traits. Low levels of genetic subdivision were reflected in an isolation by distance relationship where genetic connectivity increased with geographic proximity. This indicates extensive but not unlimited dispersal across the north-western Australian shelf. Our findings provide evidence of connectivity between current management areas, violating the assumption of multiple independent stocks. Spatial stock assessment models may be more suitable for the management of these species however demographic connectivity rates cannot be accurately estimated from the conventional population genetic approaches applied in this study. We recommend that managers aim to maintain adequate spawning biomass across current management areas, and assess stocks at finer scales, where practical.

RevDate: 2024-11-04
CmpDate: 2024-11-04

Lazar A, Phillips RP, Kivlin S, et al (2024)

Understanding the ecological versatility of Tetracladium species in temperate forest soils.

Environmental microbiology, 26(11):e70001.

Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Through amplicon sequencing of soil samples collected from 54 stands in six forest sites across the eastern United States, we identified 29 distinct Amplicon Sequence Variants (ASVs) representing Tetracladium, with large differences in relative abundance and small changes in ASV community composition among sites. Tetracladium richness was positively related to soil pH, soil temperature, total sulphur and silt content, and negatively related to plant litter quality, such as the lignin-to-nitrogen ratio and the lignocellulose index. Co-occurrence network analysis indicated negative relationships between Tetracladium and other abundant fungal groups, including ectomycorrhizal and arbuscular mycorrhizal fungi. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.

RevDate: 2024-11-04

Malik AA, Martiny JBH, Ribeiro A, et al (2024)

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition.

The ISME journal pii:7875052 [Epub ahead of print].

Microbes drive fundamental ecosystem processes such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform, yet understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates over 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes which suggested - as a trade-off - a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait-tradeoffs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

RevDate: 2024-11-04

Bradford LM, Yao L, Anastasiadis C, et al (2024)

Limit of detection of Salmonella ser. Enteritidis using culture-based versus culture-independent diagnostic approaches.

Microbiology spectrum [Epub ahead of print].

UNLABELLED: To prevent the spread of foodborne illnesses, the presence of pathogens in the food chain is monitored by government agencies and food producers. The culture-based methods currently employed are sensitive but time- and labor-intensive, leading to increasing interest in exploring culture-independent diagnostic tests (CIDTs) for pathogen detection. However, few studies quantify the relative sensitivity and reliability of these CIDTs compared to current approaches. To address this issue, we conducted a comparison of the limit of detection (LOD50) for Salmonella between a culture-based method and three CIDTs: qPCR (targeting invA and stn), metabarcode (16S) sequencing, and shotgun metagenomic sequencing. Samples of chicken feed and chicken caecal contents were spiked with S. serovar Enteritidis and subjected to culture- and DNA-based detection methods. To explore the impact of non-selective enrichment on LOD50, all samples underwent both immediate DNA extraction and overnight enrichment prior to gDNA extraction. In addition to this spike-in experiment, feed and caecal samples acquired from the field were tested with culturing, qPCR, and metabarcoding. In general, LOD50 was comparable between qPCR and shotgun sequencing methods. Overnight microbiological enrichment resulted in an improvement in LOD50 with up to a three-log decrease. However, Salmonella reads were detected in some unspiked feed samples, suggesting false-positive detection of Salmonella. In addition, the LOD50 in feeds was three logs lower than in caecal contents, underscoring the impact of background microbiota on Salmonella detection using all methods.

IMPORTANCE: The appeal of culture-independent diagnostic tests (CIDTs) is increased speed with lowered cost, as well as the potential to detect multiple pathogen species in a single analysis and to monitor other areas of concern such as antimicrobial resistance genes or virulence factors. This study provides quantitative data on the sensitivity of CIDTs relative to current approaches, which is essential for determining the feasibility of implementing these methods in pathogen surveillance programs.

RevDate: 2024-11-04

Hu H, Zhang Z, Chen B, et al (2024)

Potential health risk assessment of cyanobacteria across global lakes.

Applied and environmental microbiology [Epub ahead of print].

UNLABELLED: Cyanobacterial blooms pose environmental and health risks due to their production of toxic secondary metabolites. While current methods for assessing these risks have focused primarily on bloom frequency and intensity, the lack of comprehensive and comparable data on cyanotoxins makes it challenging to rigorously evaluate these health risks. In this study, we examined 750 metagenomic data sets collected from 103 lakes worldwide. Our analysis unveiled the diverse distributions of cyanobacterial communities and the genes responsible for cyanotoxin production across the globe. Our approach involved the integration of cyanobacterial biomass, the biosynthetic potential of cyanotoxin, and the potential effects of these toxins to establish potential cyanobacterial health risks. Our findings revealed that nearly half of the lakes assessed posed medium to high health risks associated with cyanobacteria. The regions of greatest concern were East Asia and South Asia, particularly in developing countries experiencing rapid industrialization and urbanization. Using machine learning techniques, we mapped potential cyanobacterial health risks in lakes worldwide. The model results revealed a positive correlation between potential cyanobacterial health risks and factors such as temperature, N2O emissions, and the human influence index. These findings underscore the influence of these variables on the proliferation of cyanobacterial blooms and associated risks. By introducing a novel quantitative method for monitoring potential cyanobacterial health risks on a global scale, our study contributes to the assessment and management of one of the most pressing threats to both aquatic ecosystems and human health.

IMPORTANCE: Our research introduces a novel and comprehensive approach to potential cyanobacterial health risk assessment, offering insights into risk from a toxicity perspective. The distinct geographical variations in cyanobacterial communities coupled with the intricate interplay of environmental factors underscore the complexity of managing cyanobacterial blooms at a global scale. Our systematic and targeted cyanobacterial surveillance enables a worldwide assessment of cyanobacteria-based potential health risks, providing an early warning system.

RevDate: 2024-11-04

Luu LDW, Rafique R, Payne M, et al (2024)

Deciphering Bordetella pertussis epidemiology through culture-independent multiplex amplicon and metagenomic sequencing.

Journal of clinical microbiology [Epub ahead of print].

UNLABELLED: Whooping cough (pertussis) has re-emerged despite high vaccine coverage in Australia and many other countries worldwide, partly attributable to genetic adaptation of the causative organism, Bordetella pertussis, to vaccines. Therefore, genomic surveillance has become essential to monitor circulating strains for these genetic changes. However, increasing uptake of PCR for the diagnosis of pertussis has affected the availability of cultured isolates for typing. In this study, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of B. pertussis directly from respiratory swabs. We developed a nine-target mPCR amplicon assay that could accurately type major lineages [ptxP3/non-ptxpP3, fim3A/B, fhaB3/non-fhaB3, and epidemic lineages (ELs) 1-5] circulating in Australia. Validation using DNA from isolates and 178 residual specimens collected in 2010-2012 (n = 87) and 2019 (n = 91) showed that mPCR amplicon sequencing was highly sensitive with a limit of detection of 4.6 copies [IS481 cycle threshold (Ct) 27.3]. Shotgun metagenomic sequencing was successful in genotyping B. pertussis in 84% of clinical specimens with PCR Ct < 24 and was concordant with mPCR typing results. The results revealed an expansion of EL4 strains from 2010 to 2012 to 2019 in Australia and identified unrecognized co-circulating cases of Bordetella holmesii. This study provides valuable insight into the circulating lineages in Australia prior to the COVID-19 pandemic during which border closure and other interventions reduced pertussis cases to an all-time low, and paves the way for the genomic surveillance of B. pertussis in the era of culture-independent PCR-based diagnosis.

IMPORTANCE: In this paper, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of Bordetella pertussis directly in respiratory swabs. We first developed a novel targeted mPCR amplicon sequencing assay that can type major circulating lineages and validated its accuracy and sensitivity on 178 DNA extracts from clinical swabs. We also demonstrate the feasibility of using deep metagenomic sequencing for determining strain lineage and markers of virulence, vaccine adaptation, macrolide resistance, and co-infections. Our culture-independent typing methods applied to clinical specimens revealed the expansion of a major global epidemic lineage in Australia (termed EL4) just prior to the COVID-19 pandemic. It also detected cases of previously hidden co-infections from another Bordetella species called Bordetella holmesii. These findings offer valuable insight into the circulating pertussis lineages in Australia prior to the COVID-19 pandemic during which border closure and other interventions reduced pertussis cases to an all-time low. It also provides comparative data for future surveillance as pertussis resurgence after the COVID-19 pandemic has been reported this year in Australia and many other countries. Overall, our paper demonstrates the utility, sensitivity, and specificity of mPCR amplicon and metagenomic sequencing-based culture-independent typing of B. pertussis, which not only paves the way for culture-independent genomic surveillance of B. pertussis but also for other pathogens in the era of PCR-based diagnosis.

RevDate: 2024-11-04
CmpDate: 2024-11-04

Snaith AE, Moran RA, Hall RJ, et al (2024)

Longitudinal genomic surveillance of a UK intensive care unit shows a lack of patient colonisation by multi-drug-resistant Gram-negative bacterial pathogens.

Microbial genomics, 10(11):.

Vulnerable patients in an intensive care unit (ICU) setting are at high risk of infection from bacteria including gut-colonising Escherichia coli and Klebsiella species. Complex ICU procedures often depend on successful antimicrobial treatment, underscoring the importance of understanding the extent of patient colonisation by multi-drug-resistant organisms (MDROs) in large UK ICUs. Previous work on ICUs globally uncovered high rates of colonisation by transmission of MDROs, but the situation in UK ICUs is less understood. Here, we investigated the diversity and antibiotic resistance gene (ARG) carriage of bacteria present in one of the largest UK ICUs at the Queen Elizabeth Hospital Birmingham (QEHB), focusing primarily on E. coli as both a widespread commensal and a globally disseminated multi-drug-resistant pathogen. Samples were taken during highly restrictive coronavirus disease 2019 (COVID-19) control measures from May to December 2021. Whole-genome and metagenomic sequencing were used to detect and report strain-level colonisation of patients, focusing on E. coli sequence types (STs), their colonisation dynamics and antimicrobial resistance gene carriage. We found a lack of multi-drug resistance (MDR) in the QEHB. Only one carbapenemase-producing organism was isolated, a Citrobacter carrying bla KPC-2. There was no evidence supporting the spread of this strain, and there was little evidence overall of nosocomial acquisition or circulation of colonising E. coli. Whilst 22 different E. coli STs were identified, only 1 strain of the pandemic ST131 lineage was isolated. This ST131 strain was non-MDR and was found to be a clade A strain, associated with low levels of antibiotic resistance. Overall, the QEHB ICU had very low levels of pandemic or MDR strains, a result that may be influenced in part by the strict COVID-19 control measures in place at the time. Employing some of these infection prevention and control measures where reasonable in all ICUs might therefore assist in maintaining low levels of nosocomial MDR.

RevDate: 2024-11-04

Su Q, Li YC, Zhuang DH, et al (2024)

Rewiring of uric acid metabolism in the intestine promotes high-altitude hypoxia adaptation in humans.

Molecular biology and evolution pii:7874562 [Epub ahead of print].

Adaptation to high-altitude hypoxia is characterized by systemic and organ-specific metabolic changes. This study investigates whether intestinal metabolic rewiring is a contributing factor to hypoxia adaptation. We conducted a longitudinal analysis over 108 days, with seven timepoints, examining fecal metabolomics data from a cohort of 46 healthy male adults traveling from Chongqing (a.s.l. 243 m) to Lhasa (a.s.l. 3658 m) and back. Our findings reveal that short-term hypoxia exposure significantly alters intestinal metabolic pathways, particularly those involving purines, pyrimidines, and amino acids. A notable observation was the significantly reduced level of intestinal uric acid (UA), the end product of purine metabolism, during acclimatization (also called acclimation) and in additional two long-term exposed cohorts (Han Chinese and Tibetans) residing in Shigatse, Xizang (a.s.l. 4700 m), suggesting that low intestinal UA levels facilitate adaptation to high-altitude hypoxia. Integrative analyses with gut metagenomic data showed consistent trends in intestinal UA levels and the abundance of key UA-degrading bacteria, predominantly from the Lachnospiraceae family. The sustained high abundance of these bacteria in the long-term resident cohorts underscores their essential role in maintaining low intestinal UA levels. Collectively, these findings suggest that the rewiring of intestinal UA metabolism, potentially orchestrated by gut bacteria, is crucial for enhancing human resilience and adaptability in extreme environments.

RevDate: 2024-11-04
CmpDate: 2024-11-04

Rueangmongkolrat N, Uthaipaisanwong P, Kusonmano K, et al (2024)

The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil.

PeerJ, 12:e18383.

Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.

RevDate: 2024-11-04

Jin S, Xie H, R Wang (2024)

Otitis Media Progressing to Community-Acquired Meningitis in Diabetic Patients: A Case Report of K2-ST375 hypervirulent Klebsiella pneumoniae and Literature Review.

Infection and drug resistance, 17:4707-4716.

Community-acquired Klebsiella pneumoniae meningitis (CA-KPM) can rapidly progress to invasive infection in healthy individuals. We present the case of a 54-year-old man with a history of acute suppurative otitis media and uncontrolled type 2 diabetes mellitus (T2DM), who had been treated with oral antibiotics intermittently and irregularly for one month. His symptoms did not improve and continued to worsen, leading to fever and coma. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) identified Klebsiella pneumoniae (KP) after 24 hours in the intensive care unit (ICU). Subsequent CSF culture confirmed a hypervirulent KP (hvKp) strain with capsular genotype K2 and sequence type (ST) 375. Fortunately, the patient made a full recovery with targeted antimicrobial therapy and was discharged. Despite the delayed diagnosis, the outcome was favorable. This case highlights the importance of clinicians, particularly otolaryngologists, maintaining a high index of suspicion for CA-KPM in patients with both otitis media and T2DM, emphasizing the need for timely multidisciplinary consultation.

RevDate: 2024-11-04

Kleikamp HBC, van der Zwaan R, van Valderen R, et al (2024)

NovoLign: metaproteomics by sequence alignment.

ISME communications, 4(1):ycae121.

Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.

RevDate: 2024-11-04

Chen Y, Yue Y, Wang J, et al (2023)

Microbial community dynamics and assembly mechanisms across different stages of cyanobacterial bloom in a large freshwater lake.

The Science of the total environment pii:S0048-9697(23)06834-1 [Epub ahead of print].

Cyanobacterial bloom caused by eutrophication in lakes has become one of the significant environmental problems worldwide. However, a notable research gap persists in understanding the environmental adaptation and community assembly of microbial dynamics in response to different blooming stages. Therefore, metagenomic sequencing was employed in this study to investigate alterations in the microbial community composition in water and sediment during different stages of cyanobacterial blooms in Lake Taihu. The results indicated significant spatiotemporal variations in physicochemical parameters across the early, medium, and late stages of a complete cyanobacteria bloom cycle. Diversity analysis further revealed that the temporal differences in the microbial community were substantially greater than spatial variations. Notably, during the medium-blooming stages in water, Microcystis emerged as the predominant detected cyanobacteria genus. Interestingly, the content of superoxide dismutase (SOD), malondialdehyde (MDA), and catalase (CAT) in sediment exceeded those in water by over 10 times, indicating that sediment-dwelling Cyanobacteria might constitute a crucial source of water blooms. Moreover, dissolved oxygen, pH, and water temperature were identified as the most influential environmental variables shaping the microbial community in the water. Stochasticity emerged as a prominent factor governing microbial community assembly across different bloom periods. Meanwhile, co-occurrence patterns suggested fewer interactions and instability between species in medium-blooming stages. Notably, the potential keystone phyla occupied crucial ecological niches. This research carries significant theoretical implications for managing cyanobacterial blooms in freshwater ecosystems.

RevDate: 2024-11-04

Wu X, Yu Z, Yuan S, et al (2023)

An ecological explanation for carbon source-associated denitrification performance in wastewater treatment plants.

Water research, 247:120762 pii:S0043-1354(23)01202-2 [Epub ahead of print].

The underlying mechanism associated with the roles of dosed carbon source in denitrification performance remains largely unknown. In this study, three denitrifying consortia (DNC) were constructed via evolutionary top-down enrichment method with well-defined conditions and specific carbon sources (acetate, glucose and their mixture). The reactor operation shows that nearly complete nitrate removal was achieved; however, the glucose feeding resulted in much higher concentrations of biomass and non-settable flocs. The 16S rRNA sequencing suggests that the bacterial diversity of the acetate-fed DNC was significantly higher than those of acetate/glucose-fed and glucose-fed DNCs. The dentrifying population in the acetate-fed DNC was dominated by Propionivibrio (16.1 %) and Thauera (3.4 %); whereas those of acetate/glucose- and glucose-fed DNCs were dominated by Pleomorphomonas (21.5 % and 26.3 %, respectively). Interestingly, the supernatant of acetate-fed DNC contained a high abundance of genera Thauera (averaged at 85.1 %), indicating the free-living nature of Thauera. Both PICURSt2 analysis of 16S rRNA sequencing and metagenomic analysis indicate that the acetate-fed DNC contained higher abundances of denitrifying genes; the acetate/glucose-fed and glucose-fed DNCs, in comparison, enriched genes related to glucose transportation and metabolism. Additionally, the acetate-fed DNC had better network stability than other two groups. This study adds important knowledge regarding the ecological traits of DNC, providing important clues for rational addition of carbon sources in wastewater treatment plants.

RevDate: 2024-11-04

Qiu M, Wu Z, Song J, et al (2023)

Chlorothalonil drives the antibiotic resistome in earthworm guts.

Journal of hazardous materials, 463:132831 pii:S0304-3894(23)02115-5 [Epub ahead of print].

Earthworms are recognized as carriers of pollutants; however, how fungicide residues affect microbiota and antibiotic resistance genes (ARGs) in earthworm guts has remained unclear. In this work, changes in the earthworm gut microbiome and resistome were investigated after chlorothalonil (CTL) application. Earthworm activity accelerated the dissipation of CTL in soil, while metagenomic analysis revealed that CTL altered the ARG profile, leading to an increased abundance of ARGs in earthworm guts, particularly with respect to ARG subtypes CRP and OXA-427. CTL also reduced bacterial diversity and elevated the relative abundance of the phylum Proteobacteria, including a potential ARG host, Aeromonas, which is a known pathogen. Various bacterial genera from the Actinobacteria and Proteobacteria phyla were identified as broad-spectrum hosts for ARGs in earthworm guts. CTL could increase the abundance of multidrug efflux pump genes and enhance the abundance of mobile genetic elements, especially plasmids. Various co-occurrence patterns between plasmids and ARGs were also found after CTL treatments. It is concluded that CTL may act as a selective stress for ARGs and lead to an increase in their abundance by facilitating the proliferation of potential ARG hosts and enhancing plasmid-mediated horizontal transfer frequency of ARGs in earthworm guts.

RevDate: 2024-11-04

Chowdhury RR, Dhar J, Robinson SM, et al (2023)

MACI: A machine learning-based approach to identify drug classes of antibiotic resistance genes from metagenomic data.

Computers in biology and medicine, 167:107629 pii:S0010-4825(23)01094-6 [Epub ahead of print].

Novel methodologies are now essential for identification of antibiotic resistant pathogens in order to resist them. Here, we are presenting a model, MACI (Machine learning-based Antibiotic resistance gene-specific drug Class Identification) that can take metagenomic fragments as input and predict the drug class of antibiotic resistant genes. In our study, we trained a model using the Comprehensive Antibiotic Resistance Database, containing 5138 representative sequences across 134 drug classes. Among these classes, 23 dominated, contributing 85% of the sequence data. The model achieved an average precision of 0.8389 ± 0.0747 and recall of 0.8197 ± 0.0782 for these 23 drug classes. Additionally, it exhibited higher performance (precision and recall: 0.8817 ± 0.0540 and 0.8620 ± 0.0493) for predicting multidrug resistant classes compared to single drug resistant categories (0.7923 ± 0.0669 and 0.7737 ± 0.0794). The model also showed promising results when tested on an independent data. We then analysed these 23 drug classes to identify class-specific overlapping nucleotide patterns. Five significant drug classes, viz. "Carbapenem; cephalosporin; penam", "cephalosporin", "cephamycin", "cephalosporin; monobactam; penam; penem", and "fluoroquinolone" were identified, and their patterns aligned with the functional domains of antibiotic resistance genes. These class-specific patterns play a pivotal role in rapidly identifying drug classes with antibiotic resistance genes. Further analysis revealed that bacterial species containing these five drug classes are associated with well-known multidrug resistance properties.

RevDate: 2024-11-04

Larsen S, Coleine C, Albanese D, et al (2023)

Geology and elevation shape bacterial assembly in Antarctic endolithic communities.

The Science of the total environment pii:S0048-9697(23)06677-9 [Epub ahead of print].

Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.

RevDate: 2024-11-04
CmpDate: 2024-11-04

Cansdale A, JPJ Chong (2024)

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.

Microbiome, 12(1):226.

BACKGROUND: Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.

RESULTS: To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.

CONCLUSIONS: The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.

RevDate: 2024-11-03

Zhang L, Xu W, Jiang J, et al (2024)

Metagenomic insights on promoting the removal of resistome in aerobic composting pig manure by lightly burned modified magnesite.

The Science of the total environment pii:S0048-9697(24)07258-9 [Epub ahead of print].

The antibiotic resistance genes (ARGs) have become a serious issue facing public health. In this study, light-burned magnesite with a high specific surface area at 650 °C (MS650) was used for aerobic composting, evaluating its effect on the resistome during pig manure composting. Different concentrations of MS650 reduced the abundance of the resistome, including seven high-risk ARGs, class two metal and biocide resistance genes (MBRGs), and human pathogenic bacteria (HPBs). The addition of 2.5 % MS650 (L1) in the composting had the best reduction effect on ARGs, MBRGs and HPBs. ARG and microbial community assembly are deterministic processes. Proteobacteria and Actinobacteria was the main factor associated with the decrease in ARGs, followed by virulence factor genes (VFGs, 44.2 %). The reduction in MBRGs by MS650 mainly suppressed HGT by reducing the Isfinder abundance. To summarize, MS650 is an effective method to improve emission reduction of ARGs and MBRGs. This study provided a theoretical basis for improving the engineering application potential of MS650.

RevDate: 2024-11-03

Liang W, Yan D, Zhang M, et al (2024)

Unraveling methanogenesis processes and pathways for Quaternary shallow biogenic gas in aquifer systems through geochemical, genomic and transcriptomic analyses.

The Science of the total environment pii:S0048-9697(24)07346-7 [Epub ahead of print].

Shallow biogenic gas is crucial in global warming and carbon cycling. Considering the knowledge gap in the understanding of methanogenesis and metabolic mechanisms within shallow groundwater systems, we investigated Quaternary shallow biogenic gas resources from the Hetao Basin in North China, which were previously underexplored. We systematically analyzed the genesis of gas and formation water, microbial communities, methanogenic processes, and pathways using geochemistry, genomics, and transcriptomics. Our findings indicated that active freshwater environments are conducive to microbial activity and the generation of primary microbial gases. A diverse range of microbes with functions, such as hydrolysis (e.g., Caulobacter), acidogenesis, and hydrogen production (e.g., Sediminibacterium), synergistically contributed to the methanogenic process. Methanogens predominantly comprised hydrogenotrophic methanogens (e.g., Methanobacteriales), although H2-dependent methylotrophic methanogens (e.g., Methanofastidiosa) were also prevalent. The metabolic processes of the different methanogenic pathways were revealed based on functional gene analysis and mapping results. Furthermore, the composition of the community structure, functional predictions, metagenomics, and metatranscriptomics underscored the contribution of the hydrogenotrophic pathway, which ranged from 52.22 % to 79.23 %. The aceticlastic pathway exhibited high gene abundance and was primarily associated with methylotrophs and other potential pathways. The H2-dependent methylotrophic methanogenesis pathway was constrained by low metabolic activity. By revealing the methane production mechanism of biogenic gas in shallow aquifer systems, this study provides a new perspective and profound comprehension of its ecological and environmental implications worldwide.

RevDate: 2024-11-03

Li T, Coker OO, Sun Y, et al (2024)

Multi-cohort analysis reveals altered archaea in colorectal cancer fecal samples across populations.

Gastroenterology pii:S0016-5085(24)05596-3 [Epub ahead of print].

BACKGROUND AND AIM: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts from 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls (HC)). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria and methanogenic functions were analyzed. Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HC, adenoma patients to CRC patients with Methanobacteriota phylum enriched while order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, while 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in CRC patients across multiple cohorts. Among them, M. stadmanae, Methanobrevibacter_A sp900314695 and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in CRC patients. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating CRC patients from healthy individuals with AUC ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, adenoma patients and CRC patients. Archaeal biomarkers, combined with bacterial features, have potential as non-invasive diagnostic biomarkers for CRC.

RevDate: 2024-11-03

Witkabel P, C Abendroth (2024)

A systematic literature review of microbial ANAMMOX consortia in UASB/ EGSB-reactors.

Chemosphere pii:S0045-6535(24)02530-X [Epub ahead of print].

Anaerobic ammonium oxidation (ANAMMOX) poses an emerging research field as it can outstand previous processes of biological wastewater treatment in terms of efficiency and costs. Anammox bacteria have the ability to metabolise NH4[+] and NO2[-] to produce N2 under anaerobic conditions. Despite numerous studies, there is a lack of research on the co-occurrence and interrelationship of the predominant microbes that inhabit anammox-related processes. This systematic literature review follows the PSALSAR approach to assess metagenomic data on anammox bacteria and functional microbes in upstream reactors. Essential information on the physiology, metabolic pathways and inhibitory effects of anammox bacteria are reviewed and functional bacteria such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), ammonia-oxidising Archaea (AOA) and denitrifying bacteria are identified. Candidatus Kuenenia and Candidatus Brocadia were the most frequently sequenced genera in the observed literature. Pseudomonadota, Chloroflexota and Bacteroidota were prevalent regardless of crucial operational parameters and configurations that affect the microbial community. Interrelationship analysis revealed a positive association between the versatility of a phylum's metabolism and its presence in the observed wastewater treatment literature. Several groups, such as Calditrichota, Myxococcota and Deinococcota are highly underrepresented, a finding that should be investigated in more detail. No evidence was found to suggest that high anammox ratios are correlated with high nitrogen removal efficiencies, as some studies found high efficiency despite low anammox abundance (<1%).

RevDate: 2024-11-03

Gregoris K, WH Pope (2024)

Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea.

Journal of microbiological methods pii:S0167-7012(24)00177-5 [Epub ahead of print].

Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.

RevDate: 2024-11-03

Ji J, Zhao Y, Wu G, et al (2024)

Responses of endogenous partial denitrification process to acetate and propionate as carbon sources: Nitrite accumulation performance, microbial community dynamic changes, and metagenomic insights.

Water research, 268(Pt A):122680 pii:S0043-1354(24)01579-3 [Epub ahead of print].

Endogenous partial denitrification (EPD) offered a promising pathway for supplying nitrite to anammox, and it also enabled energy-efficient and cost-effective nitrogen removal. However, information about the impact of different carbon sources on the EPD system was limited, and the metabolic mechanisms remained unclear. This study operated the EPD system for 180 days with various acetate and propionate ratios over eight phases. The nitrate-to-nitrite transformation ratio (NTR) decreased from 81.7 % to 0.4 % as the acetate/propionate (Ac/Pr) ratio shifted from 3:0 to 0:3, but the NTR returned to 86.1 % after propionate was replaced with acetate. Typical cycles indicated that PHB (126.8 and 133.9 mg COD/g VSS, respectively) was mainly stored, facilitating a higher NTR (87.8 % and 67.7 %, respectively) on days 58 and 180 in the presence of acetate. In contrast, on day 158 in the presence of propionate, PHV (84.8 mg COD/g VSS) was predominantly stored, resulting in negligible nitrite accumulation (0.2 mg N/L). Metagenomic analysis revealed that the microbial community structure did not significantly change, and the (narGHI+napAB)/nirKS ratio consistently exceeded 7:2, despite variations in the carbon source. Compared with acetate, propionate as carbon source reduced the abundance of genes encoding NADH-producing enzymes (e.g., mdh), likely owing to a shift in PHAs synthesis and degradation pathways. Consequently, limited NADH affected electron distribution and transfer rates, thereby decreasing the nitrate reduction rate and causing nitrite produced by narGHI and napAB to be immediately reduced by nirKS. This study provided new insights and guidance for EPD systems to manage the conditions of carbon deficiency or complex carbon sources.

RevDate: 2024-11-03

Guo XP, Chen XJ, Sidikjan N, et al (2024)

Silver nanoparticles regulate antibiotic resistance genes by shifting bacterial community and generating anti-silver genes in estuarine biofilms.

Aquatic toxicology (Amsterdam, Netherlands), 276:107131 pii:S0166-445X(24)00301-1 [Epub ahead of print].

Biofilms are thought to be sinks for antibiotic resistance genes (ARGs) and nanoparticles (NPs), however, studies on the interactions between NPs and ARGs in biofilms are limited. This study focused on the occurrence and regulatory mechanisms of ARGs during the formation of biofilms with continuous treatment of zero-valent silver nanoparticles (Ag[0]-NPs) and Ag ions at an environmental concentration of 10 µg/L in the Yangtze Estuary. The biofilms could enrich large amounts of Ag, with the highest concentration of 97.60 mg/kg and 111.08 mg/kg in the Ag[0]-NPs and Ag ions group at 28 days. Compared to the blank at 28 days, the abundance of ARGs was reduced 2.2 times in the Ag[0]-NPs group, whereas it increased 1.3 times in the Ag ion group. Ag[0]-NPs and Ag ions induced the production of silver resistance genes (SRGs) or selected bacteria with SRGs in biofilms. Based on machine learning, the bacterial community, SRGs, and Ag concentration were the top three dominant regulators of ARGs, with 27.74 %, 25.57 %, and 17.93 % contributions, respectively. Structural equation modeling revealed that Ag could indirectly regulate ARGs by regulating the bacterial community in the Ag[0]-NPs group. Metagenomic sequencing further showed that most of the decreased ARGs were hosted by Betaproteobacteria in the Ag[0]-NPs groups. According to the KEGG pathway database, the possible molecular mechanism of Ag[0]-NPs/Ag ions regulating ARGs may be through the two-component system (arlS/silS-arlR) and beta-lactam resistance system (mexI-mexV-oprM/oprZ/smeF). Overall, this study provides new insights into the effects of Ag[0]-NPs at environmental concentrations on the ecological environment, especially regarding the mechanism of regulating ARGs in estuarine biofilms.

RevDate: 2024-11-03
CmpDate: 2024-11-03

Jiang L, Han L, Zhong Y, et al (2024)

High utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing approach for etiological diagnosis of pneumonia.

BMC infectious diseases, 24(1):1232.

BACKGROUND: For patients with pneumonia, the rapid detection of pathogens is still a major global problem in clinical practice because traditional diagnostic techniques for infection are time-consuming and insensitive. Metagenomic next-generation sequencing (mNGS) is a novel technique that has the potential to improve pathogen diagnosis. This study aimed to investigate the microbiological diagnostic ability of mNGS compared with conventional culture and to determine the optimal time to test patients for pneumonia.

METHODS: A prospective study using data from June 2020 to June 2021 was performed at a tertiary teaching hospital in China. We included 56 patients from all adult patients with a clinical diagnosis of pneumonia. Blood and bronchoalveolar lavage fluid (BALF) samples were taken for simultaneous mNGS and conventional culture testing.

RESULTS: All 56 patients underwent both conventional culture and mNGS. Of these patients, 37 were diagnosed with severe pneumonia and 17 were diagnosed with non-severe pneumonia. The top three pathogenic bacteria detected by mNGS were Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Enterococcus faecium was detected more frequently in the non-severe pneumonia group (4 vs. 0, p < 0.05). The findings revealed that the detection rate of mNGS (84%) was superior to that of conventional culture methods (48%). Notably, the percentage of mNGS-positive BALF samples (46/56, 82.14%) was significantly greater than that of blood samples (27/56, 48.21%). The etiological comparison demonstrated that mNGS-positive samples, which received clinical approval, tended to be associated with a more normalized temperature, lower PCO2 levels, and a higher SOFA score than mNGS-negative samples (p = 0.022, p = 0.0.028, and p = 0.038, respectively).

CONCLUSIONS: In this study, we discovered that the etiology of lung infections frequently involves multiple pathogens. The use of mNGS in BALF is instrumental for detecting nonviral pathogens associated with lung infections. Although the rate of positive blood NGS results is significantly influenced by various clinical factors, for patients suspected of having viral, Legionella, or tsutsugamushi infections, plasma mNGS could serve as a complementary diagnostic tool.

RevDate: 2024-11-03
CmpDate: 2024-11-03

Yao QH, Zhi HL, Xia XJ, et al (2024)

Primary cutaneous infections with non-tuberculous mycobacteria: a report of 6 cases.

BMC infectious diseases, 24(1):1231.

BACKGROUND: The incidence of non-tuberculous mycobacterium infection has shown a gradual increasing trend in recent years, among which cutaneous manifestations as an important aspect. This study aimed to describe the clinical features and microbiological findings in 6 cases of primary cutaneous nontuberculous mycobacterium infection.

METHODS: In this retrospective study from June 2021 to June 2022, the clinical data and microbiological results of six cases diagnosed with primary cutaneous non-tuberculous mycobacterium infection in department of dermatology, Hangzhou Third People's Hospital were analyzed.

RESULTS: All six cases were primary cutaneous non-tuberculous mycobacterium infections, four of which had a history of trauma or exposure, and two had an underlying disease that could lead to compromised immunity. All patients presented with erythema nodular skin lesions, four on the upper or lower extremities, one on the face, and one on the right hip. The histopathological findings of five patients who underwent biopsy were granulomatous inflammatory changes with mixed infiltration. Laboratory cultures using tissue or tissue fluid were all successful, including four Mycobacterium marinum, one Mycobacterium abscessus, and one Mycobacterium avium. Metagenomics next-generation sequencing detected results consistent with culture colonies in only two cases. With the exception of case 4, all patients responded well to oral medication, with a course of treatment ranging from 4 months to 1 year, and the prognosis was good.

CONCLUSIONS: The clinical features of primary cutaneous non-tuberculous mycobacterium infection are often lacking in specificity, and the identification of related strains is difficult for a variety of reasons. Although the results of metagenomics next-generation sequencing are useful for pathogen spectrum identification, its diagnostic value should be carefully reevaluated under certain circumstances. Patients with suspected triggers who do not respond well to conventional treatments should be suspected as atypical infection and potential immunosuppression. If diagnosed and treated promptly, the prognosis of primary cutaneous non-tuberculous mycobacterium infection is generally good.

RevDate: 2024-11-03
CmpDate: 2024-11-03

Qi M, Du Y, Guan J, et al (2024)

The clinical management and efficacy of metagenomic next-generation sequencing in patients with pyogenic spinal infection: a single-center cohort study.

Journal of orthopaedic surgery and research, 19(1):716.

OBJECTIVE: This study aims to evaluate the clinical management and effectiveness of metagenomic next-generation sequencing (mNGS) in patients with pyogenic spinal infections.

METHODS: We conducted a retrospective review of 17 patients diagnosed with pyogenic spinal infections and treated at our institution between October 2022 and February 2024. The cohort included 8 males and 9 females, with a mean age of 63.59 ± 10.18 years (range: 41-71 years). The infections comprised 9 epidural abscesses, 6 intervertebral space infections, and 2 deep abscesses. All patients underwent open surgical procedures and mNGS-based bacterial identification using intraoperative pus or tissue specimens, in addition to conventional blood bacterial cultures. Clinical outcomes were assessed using CRP, PCT, WBC inflammatory markers, and VAS scores postoperatively.

RESULTS: All 17 patients with pyogenic spinal infections underwent open surgery and mNGS bacterial detection at our institution. Among the 17 patients, mNGS yielded positive results in 14 cases (82.4%), significantly higher than the 5.9% positivity rate of conventional bacterial cultures (p < 0.001). The mNGS test time was notably shorter than conventional cultures (1.0 vs. 5.88 days, p < 0.001). Postoperative antibiotic therapy was adjusted based on mNGS findings. There were significant reductions in postoperative VAS, WBC, PCT, and CRP values compared to preoperative levels (p < 0.01).

CONCLUSION: Metagenomic next-generation sequencing is effective in managing pyogenic spinal infections by facilitating rapid and sensitive detection of pathogens. This technique improves the timeliness and accuracy of diagnosis, highlighting its potential for broader clinical use.

RevDate: 2024-11-03
CmpDate: 2024-11-03

Geat N, Singh D, Saha P, et al (2024)

Deciphering Phyllomicrobiome of Cauliflower Leaf: Revelation by Metagenomic and Microbiological Analysis of Tolerant and Susceptible Genotypes Against Black Rot Disease.

Current microbiology, 81(12):439.

Understanding the phyllomicrobiome dynamics in cauliflower plants holds significant promise for enhancing crop resilience against black rot disease, caused by Xanthomonas campestris pv. campestris. In this study, the culturable microbiome and metagenomic profile of tolerant (BR-161) and susceptible (Pusa Sharad) cauliflower genotypes were investigated to elucidate microbial interactions associated with disease tolerance. Isolation of phyllospheric bacteria from asymptomatic and black rot disease symptomatic leaves of tolerant and susceptible cultivars yielded 46 diverse bacterial isolates. Molecular identification via 16S rRNA sequencing revealed differences in the diversity of microbial taxa between genotypes and health conditions. Metagenomic profiling using next-generation sequencing elucidated distinct microbial communities, with higher diversity observed in black rot disease symptomatic leaf of BR-161. Alpha and beta diversity indices highlighted differences in microbial community structure and composition between genotypes and health conditions. Taxonomic analysis revealed a core microbiome consisting of genera such as Xanthomonas, Psychrobacillus, Lactobacillus, and Pseudomonas across all the samples. Validation through microbiological methods confirmed the presence of these key genera. The findings provide novel insights into the phyllomicrobiome of black rot-tolerant and susceptible genotypes of cauliflower. Harnessing beneficial microbial communities identified in this study offers promising avenues for developing sustainable strategies to manage black rot disease and enhance cauliflower crop health and productivity.

RevDate: 2024-11-03
CmpDate: 2024-11-03

Li X, Cheng R, Zhang C, et al (2024)

Genomic diversity of phages infecting the globally widespread genus Sulfurimonas.

Communications biology, 7(1):1428.

The widespread bacterial genus Sulfurimonas is metabolically versatile and occupies a key ecological niche in different habitats, but its interaction with bacteriophages remains unexplored. Here we systematically investigated the genetic diversity, taxonomy and interaction patterns of Sulfurimonas-associated phages based on sequenced microbial genomes and metagenomes. High-confidence phage contigs related to Sulfurimonas were retrieved from various ecosystems, clustered into 61 viral operational taxonomic units across three viral realms, including Duplodnaviria, Monodnaviria and Varidnaviria. Head-tail phages of Caudoviricetes were assigned to 19 genus-level viral clusters, the majority of which were distantly related to known viruses. Notably, diverse double jelly-roll viruses and inoviruses were also linked to Sulfurimonas, representing two commonly overlooked phage groups. Historical and current phage infections were revealed, implying viral impact on the evolution of host adaptive immunity. Additionally, phages carrying auxiliary metabolic genes might benefit hosts by compensating or augmenting sulfur metabolism. This study highlights the diversity and novelty of Sulfurimonas-associated phages with divergent tailless lineages, providing basis for further investigation of phage-host interactions within this genus.

RevDate: 2024-11-02
CmpDate: 2024-11-02

De Luca D, Piredda R, Scamardella S, et al (2024)

Taxonomic and metabolic characterisation of biofilms colonising Roman stuccoes at Baia's thermal baths and restoration strategies.

Scientific reports, 14(1):26290.

Stuccoes are very delicate decorative elements of Roman age. Very few of them survived almost intact to present days and, for this reason, they are of great interest to restorers and conservators. In this study, we combined metabarcoding and untargeted metabolomics to characterise the taxonomic and metabolic profiles of the microorganisms forming biofilms on the stuccoes located on the ceiling of the laconicum, a small thermal environment in the archaeological park of Baia (southern Italy). We found that some samples were dominated by bacteria while others by eukaryotes. Additionally, we observed high heterogeneity in the type and abundance of bacterial taxa, while the eukaryotic communities, except in one sample (at prevalence of fungi), were dominated by green algae. The metabolic profiles were comparable across samples, with lipids, lipid-like molecules and carbohydrates accounting for roughly the 50% of metabolites. In vitro and in vivo tests to remove biofilms on stuccoes using essential oils blends were successful at a 50% dilution for one hour and half. This integrative study advanced our knowledge on taxonomic and metabolic profiles of biofilms on ancient stuccoes and highlighted the potential impacts of these techniques in the field of cultural heritage conservation.

RevDate: 2024-11-02

Xiao C, Ide K, Matsunaga H, et al (2024)

Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan.

Journal of bioscience and bioengineering pii:S1389-1723(24)00281-0 [Epub ahead of print].

Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for ErmB, ErmF, ErmG, tetQ, tet (W/N/W), aadA2, and adeF, including gut-associated bacteria (e.g., Prevotella, Bacteroides, Arcobacter) and indigenous aquatic microbes (e.g., Limnohabitans and C39). In addition, Pseudarcobacter (a later synonym of Arcobater) was identified as a host for adeF, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.

RevDate: 2024-11-02

Zhao Y, Zhang J, Zheng Y, et al (2024)

Overlooked dissemination risks of antimicrobial resistance through green tide proliferation.

Water research, 268(Pt B):122714 pii:S0043-1354(24)01613-0 [Epub ahead of print].

Green tides, particularly those induced by Enteromorpha, pose significant environmental challenges, exacerbated by climate change, coastal eutrophication, and other anthropogenic impacts. More concerningly, these blooms may influence the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) within ecosystems. However, the manner in which Enteromorpha blooms affect the distribution and spread of antimicrobial resistance (AMR) remains uncertain. This study investigated ARG profiles, dynamic composition, and associated health risks within the Enteromorpha phycosphere and surrounding seawater in typical bays (Jiaozhou, Aoshan, and Lingshan) in the South Yellow Sea. The Enteromorpha phycosphere exhibited significantly higher ARG abundance (p < 0.05) but lower diversity compared to the surrounding seawater. Source-tracking and metagenomic analyses revealed that the phycosphere was the main contributor to the resistome of surrounding seawater. Moreover, resistant pathogens, especially ESKAPE pathogens, with horizontal gene transfer (HGT) potential, were more abundant in the phycosphere than in the surrounding seawater. The phycosphere released high-risk ARGs to the surrounding seawater during Enteromorpha blooms, posing serious health and ecological AMR risks in marine environments. This study highlights the significant role of Enteromorpha blooms in ARG spread and associated risks, urging a reassessment of AMR burden from a public health perspective.

RevDate: 2024-11-02

Berckx F, Van Nguyen T, Hilker R, et al (2024)

Host dependent specialized metabolism of nitrogen export in actinorhizal nodules induced by Frankia cluster-2.

Journal of experimental botany pii:7866822 [Epub ahead of print].

Frankia cluster-2 strains are diazotrophs that engage in root nodule symbiosis with actinorhizal plants of the Cucurbitales and the Rosales. Previous studies have shown that an assimilated nitrogen source, presumably arginine, is exported to the host in nodules of Datisca glomerata (Cucurbitales), while a different metabolite is exported in the nodules of Ceanothus thyrsiflorus (Rosales). To investigate if an assimilated nitrogen form is commonly exported to the host by cluster-2 strains, and which metabolite would be exported in Ceanothus, we analysed gene expression levels, metabolite profiles, and enzyme activities in nodules. We conclude that the export of assimilated nitrogen in symbiosis seems to be a common feature for Frankia cluster-2 strains, but which source is host-dependent. The export of assimilated ammonium to the host suggests that 2-oxoglutarate is drawn from the TCA cycle at a high rate. This specialised metabolism obviates the need for the reductive branch of the TCA cycle. We found several genes encoding enzymes of the central carbon and nitrogen metabolism were lacking in Frankia cluster-2 genomes: the glyoxylate shunt and succinate semialdehyde dehydrogenase. This led to a linearization of the TCA cycle, and we hypothesize this could explain the low saprotrophic potential of Frankia cluster-2.

RevDate: 2024-11-02
CmpDate: 2024-11-02

Kosch TA, Torres-Sánchez M, Liedtke HC, et al (2024)

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

BMC genomics, 25(1):1025.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

RevDate: 2024-11-02
CmpDate: 2024-11-02

Wardi M, Lemkhente Z, Alla AA, et al (2024)

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach.

Scientific reports, 14(1):26328.

Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.

RevDate: 2024-11-02
CmpDate: 2024-11-02

Sato T, Abe K, Koseki J, et al (2024)

Survivability and life support in sealed mini-ecosystems with simulated planetary soils.

Scientific reports, 14(1):26322.

Establishing a sustainable life-support system for space exploration is a formidable challenge due to the vast distances, high costs, and environmental differences from Earth. Building upon the lessons from the Biosphere 2 experiment, we introduce the novel "Ecosphere" and "Biosealed" systems, self-sustaining ecosystems within customizable, enclosed containers. These systems incorporate terrestrial ecosystems and groundwater layers, offering a potential model for transplanting Earth-like biomes to extraterrestrial environments. Over 4 years, we conducted rigorous experiments and analyses to understand the dynamics of these enclosed ecosystems. We successfully mitigated moisture deficiency, a major obstacle to plant growth, by incorporating groundwater layers. Additionally, we quantified microbial communities proliferating in specific soils, including simulated lunar and Ryugu asteroid regolith, enhance plant cultivation in space environments. Metagenomic analysis of these simulated space soils revealed diverse microbial populations and their crucial role in plant growth and ecosystem stability. Notably, we identified symbiotic relationships between plants and Cyanobacteria, enhancing oxygen production, and demonstrated the potential of LED lighting as an alternative light source for plant cultivation in sun-limited space missions. We also confirmed the survival of fruit flies within these systems, relying on plant-produced oxygen and photosynthetic bacteria. Our research provides a comprehensive framework for developing future space life-support systems. The novelty of our work lies in the unique design of our enclosed ecosystems, incorporating groundwater layers and simulated extraterrestrial soils, and the detailed analysis of microbial communities within these systems. These findings offer valuable insights into the challenges and potential solutions for establishing sustainable human habitats in space, including the importance of microbial management and potential health concerns related to microbial exposure.

RevDate: 2024-11-01

Williams AD, Leung VW, Tang JW, et al (2024)

Ancient environmental microbiomes and the cryosphere.

Trends in microbiology pii:S0966-842X(24)00253-1 [Epub ahead of print].

In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.

RevDate: 2024-11-02

Tang X, Yao Q, Jiang X, et al (2024)

Response of ammonium transformation in bioanodes to potential regulation: Performance, electromicrobiome and implications.

Bioresource technology, 415:131731 pii:S0960-8524(24)01435-4 [Epub ahead of print].

Understanding how potential regulation affects ammonium transformation in bioanodes is crucial for promoting their application. This study explored the performance, electrochemical properties, electromicrobiome of bioanodes across potentials from 0.0 V to 0.4 V vs. standard hydrogen electrode (SHE). Higher anode potentials enhanced the performance of electroactive biofilms and ammonium removal but suppressed nitrite oxidation while favoring dissimilatory nitrate reduction (DNRA), leading to increased nitrite accumulation. A reduction in nitrite-oxidizing bacteria (NOB) and an increase in DNRA-related genes resulted in an optimal nitrite-to-ammonium ratio of 1.32 for the Anammox process. Higher anodic potentials (0.3 and 0.4 V) were less effective for TN removal than lower potentials (0, 0.1, and 0.2 V), likely due to increased NOB and denitrification genes at lower potentials enhancing nitrite oxidation and denitrification. These findings indicate that regulating anodic potential effectively directs ammonium transformation in bioanodes, optimizing its conversion to N2 or nitrite.

RevDate: 2024-11-01

Zhang H, Cheng S, Yan W, et al (2024)

Interplay between vanadium distribution and microbial community in soil-plant system.

Journal of hazardous materials, 480:136303 pii:S0304-3894(24)02882-6 [Epub ahead of print].

Soil-plant system play an essential role in distribution and transformation of vanadium (V). V shapes the diversity of soil communities, while soil microorganisms mediate V transformation. Plants also absorb V from surrounding soil. However, the study of microbial response to V stress in different soil-plant compartments is limited, and the metabolic functions driving V transformation across these systems remain elusive. The study investigates the distribution of V in soil-plant systems nearby a V smelter. 16S rRNA sequencing and metagenomics are utilized to reveal the microbial adaptation and V transformation in bulk soil, rhizosphere, and endosphere. Bothriochloa ischaemum (L.) Keng. (BK) exhibits higher phytoextraction potential (TF = 0.74 ± 0.26). Environmental variables, including pH, V, OM, and AP, show significant (p < 0.05) influence in soil community composition, with homogeneous selection governing the assembly processes in bulk soil and rhizosphere, while stochastic process dominates endospheric assembly. Metagenomic investigation revealed a coordinated metabolic pathway between functional taxa in soil and plants, which lead to root uptake and translocation. V stress is mitigated through Nocardioide, Microvirga, and Solirubrobacter, putatively harboring V(V) reduction genes n arG and mtrC in soil. In rhizosphere, citrate synthase gltA and alkaline phosphatase phoD exhibit functional potential to facilitate formation of V-complexation to increase V mobility. In endoshere, endophytic Enterobacter further detoxifies V(V), and likely promotes V translocation through siderophore biosynthesis gene, iucA. These findings enhance our understanding on interplay between V and microbial community in soil-plant systems, which is instrumental in developing mitigation plan for V contaminated sites.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Achudhan AB, LM Saleena (2024)

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.

World journal of microbiology & biotechnology, 40(12):370.

Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Hasegawa-Takano M, Hosaka T, Kojima K, et al (2024)

Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria.

The ISME journal, 18(1):.

Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored. Here, we used a metagenomic mining approach, which led to the identification of a novel rhodopsin clade unique to cyanobacteria, cyanorhodopsin-II (CyR-II). CyR-IIs function as light-driven outward H+ pumps. CyR-IIs, together with previously identified cyanorhodopsins (CyRs) and cyanobacterial halorhodopsins (CyHRs), constitute cyanobacterial ion-pumping rhodopsins (CyipRs), a phylogenetically distinct family of rhodopsins. The CyR-II clade is further divided into two subclades, YCyR-II and GCyR-II, based on their specific absorption wavelength. YCyR-II absorbed yellow light (λmax = 570 nm), whereas GCyR-II absorbed green light (λmax = 550 nm). X-ray crystallography and mutational analysis revealed that the difference in absorption wavelengths is attributable to slight changes in the side chain structure near the retinal chromophore. The evolutionary trajectory of cyanobacterial rhodopsins suggests that the function and light-absorbing range of these rhodopsins have been adapted to a wide range of habitats with variable light and environmental conditions. Collectively, these findings shed light on the importance of rhodopsins in the evolution and environmental adaptation of cyanobacteria.

RevDate: 2024-11-01

Feng L, Guo Z, Yao W, et al (2024)

Metagenomics and Untargeted Metabolomics Analysis Revealed the Probiotic and Postbiotic Derived from Lactiplantibacillus plantarum DPUL F232 Alleviate Whey Protein-Induced Food Allergy by Reshaping Gut Microbiota and Regulating Key Metabolites.

Journal of agricultural and food chemistry [Epub ahead of print].

Postbiotics have emerged as a promising alternative to probiotics. However, it remains unclear whether postbiotics can exert regulatory effects on intestinal flora and metabolism as probiotics. Thus, we investigated the effects of probiotic and postbiotic in rats with whey protein-induced food allergy, which demonstrated that postbiotic intervention effectively alleviated allergy symptoms, reduced serum immunoglobulin E (IgE) and mast cell protease-1 (mMCP-1) levels, and regulated the type helper 1 cell/2 cell (Th1/Th2) balance in both serum and spleen. Metagenomic analysis revealed that postbiotics induced more significant changes in intestinal flora. Untargeted metabolomics analysis showed that both probiotics and postbiotics significantly up-regulated various differential metabolites, which were negatively correlated with immune indices, including malvidin-3-glucoside, 3,4-dihydroxymandelic acid, nicotinamide, triterpenoids, pirbuterol, and 4-hydroxybenzoic acid. This study confirms that postbiotics can alleviate food allergies and regulate intestinal flora and metabolites, which provides a valuable reference for the use of postbiotics in mitigating allergic diseases through gut microbiota and metabolite modulation.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Gao L, Rao MPN, Liu YH, et al (2024)

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.

Microbial ecology, 87(1):135.

Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.

RevDate: 2024-11-01

Virachabadoss VRA, Appavoo MS, Paramasivam KS, et al (2024)

The addition of humic acid into soil contaminated with microplastics enhanced the growth of black gram (Vigna mungo L. Hepper) and modified the rhizosphere microbial community.

Environmental science and pollution research international [Epub ahead of print].

Microplastics have polluted agricultural soils, posing a substantial risk to crop productivity. Moreover, the presence of microplastic pollution has caused a disturbance in the composition of the microbial community in the soil surrounding plant roots, therefore impacting the growth of beneficial bacteria. A study was conducted to examine if humic acid (HA) can counteract the harmful effects of microplastics (MPs) on the growth of black gram crops and the composition of the rhizosphere soil microbial community, to reduce the negative impacts of microplastics on these microorganisms and crops. The research was carried out using mud pots and the plastic utilized for the experiment consisted of 60% high-density polyethylene (HDPE) and 40% polypropylene (PP). The soil was enriched with lignite-based potassium humate, which had a pH range of 8.0-9.5 and with 65% humic acid. The experiment consisted of six treatments: T1, which served as the control without HA and MP; T2, which involved the use of HA at a concentration of 0.15% w/w; T3, which involved the use of MP at a concentration of 0.2% w/w; T4, which involved the use of MP at a concentration of 0.4% w/w; T5, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.2% w/w; and T6, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.4% w/w. The plant growth characteristics, including germination percentage, nodule number, and chlorophyll content, were measured. In addition, the DNA obtained from the rhizosphere soil was analyzed using metagenomics techniques to investigate the organization of the microbial population. Seedlings in soil polluted with MP exhibited delayed germination compared to seedlings in uncontaminated soil. Following 60 days of growth, the soil samples treated with T5 (0.2% MP and 0.15% HA w/w) had the highest population of bacteria and rhizobium, with counts 5.58 ± 0.02 and 4.90 ± 0.02 CFU g[-1] soil. The plants cultivated in T5 had the most elevated chlorophyll-a concentration (1.340 ± 0.06 mg g[-1]), and chlorophyll-b concentration (0.62 ± 0.02 mg g[-1]) while those cultivated in T3 displayed the lowest concentration of chlorophyll-a (0.59 ± 0.02 mg g[-1]) and chlorophyll-b (0.21 ± 0.04 mg g[-1]). Within the phylum, Proteobacteria had the highest prevalence in all treatments. However, when the soil was polluted with MPs, its relative abundance was reduced by 8.4% compared to the control treatment (T1). Conversely, treatment T5 had a 3.76% rise in relative abundance when compared to treatment T3. The predominant taxa found in soil polluted with MP were Sphingomonas and Bacillus, accounting for 19.3% of the total. Sphingomonas was the predominant genus (21.2%) in soil polluted with MP and supplemented with humic acid. Humic acid can be used as a soil amendment to mitigate the negative effects of MPs and enhance their positive advantages. Research has demonstrated that incorporating humic acid into soil is a viable method for maintaining the long-term integrity of soil's physical, chemical, and biological characteristics.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Fernandez-Garcia MD, Garcia-Ibañez N, Camacho J, et al (2024)

Enhanced echovirus 11 genomic surveillance in neonatal infections in Spain following a European alert reveals new recombinant forms linked to severe cases, 2019 to 2023.

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 29(44):.

BackgroundIn 2023, a European alert was issued regarding an increase in severe enterovirus (EV) neonatal infections associated with echovirus 11 (E11) new lineage 1.AimTo analyse E11-positive cases between 2019 and 2023 to investigate whether the new lineage 1 circulated in Spain causing severe neonatal infections.MethodsEV-positive samples from hospitalised cases are sent for typing to the National Reference Enterovirus Laboratory. Available samples from 2022-23 were subjected to metagenomic next-generation sequencing.ResultsOf 1,288 samples genotyped, 103 were E11-positive (98 patients: 6 adults, 33 neonates, 89 children under 6 years; male to female ratio 1.9). E11 detection rate was similar before and after detection of the new lineage 1 in Spain in June 2022 (9.7% in 2019 vs 10.6% in 2023). The proportion of E11-infected ICU-admitted neonates in 2019-2022 (2/7) vs 2022-2023 (5/12) did not significantly differ (p = 0.65). In severe neonatal infections, 4/7 E11 strains were not linked to the new lineage 1. The three novel E11 recombinant genomes were associated with severe (n = 2) and non-severe (n = 1) cases from 2022-2023 and clustered outside the new lineage 1. Coinfecting pathogenic viruses were present in four of 10 E11-positive samples.ConclusionThe emergence of the new lineage 1 is not linked with an increase in incidence or severity of neonatal E11 infections in Spain. The detection of two novel E11 recombinants associated with severe disease warrants enhancing genomic and clinical surveillance.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Yang Q, Chen X, Kou G, et al (2024)

A rare case of prostatic malakoplakia with multidrug-resistant Escherichia coli: a case report.

BMC infectious diseases, 24(1):1226.

Prostatic malakoplakia is an uncommon chronic inflammatory disorder, tumor-like but non-cancerous, the diagnosis of which pivots crucially on the identification of characteristic Michaelis-Gutmann bodies within the pathological tissue. We hereby present an inaugural case report of prostatic malakoplakia concurrent with sepsis caused by multidrug-resistant Escherichia coli, verified through blood culture and metagenomic next-generation sequencing (mNGS). The pathogenesis might be associated with infections by Escherichia coli, immune system irregularities, or lysosomal dysfunction. Although the patient had no chronic underlying diseases, he presented early with sepsis and multi-organ dysfunction. This case emphasizes the imperative to further investigate the association between malakoplakia and Escherichia coli, the necessity for prompt diagnosis, and the supportive role of mNGS, and the treatment strategy focuses on rapid control of infection and systemic inflammatory response.

RevDate: 2024-11-01

Neugent ML, Hulyalkar NV, Ghosh D, et al (2024)

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.

bioRxiv : the preprint server for biology pii:2024.10.22.619727.

Recurrent urinary tract infections (rUTIs) are a major clinical challenge in postmenopausal women and their increasing prevalence underscores the need to define interactions between the host and the urinary microbiome that may underlie rUTI susceptibility. A body of work has identified the taxonomic profile of the female urinary microbiome associate with aging, menopause, and urinay disease. However, how this microbial community engages with the host niche, including the local biochemical environment of the urogenital tract, in health and disease is yet to be fully defined. This study directly assesses differences in the biochemical environment of the urine, or biochemical ecology, associated with recurrent urinary tract infection (UTI) and defines a microbe-metabolite association network of the female urinary microbiome. By integrating metagenomic and metabolomic data collected from a controlled cohort of women with rUTI, we find that distinct metabolites, such as methionine sulfoxide (Met-SO) and trimethylamine oxide (TMAO), are associated with differences in urinary microbiome diversity. We observe associations between microbial and biochemical beta diversity and unique metabolic networks of uropathogenic Escherichia coli and uroprotective Lactobacillus species, highlighting potential metabolite-driven ecological shifts that may influence UTI susceptibility. We identify a urinary lipid signature of active rUTI that can accurately distinguish (AUC = 0.987) cases controls. Finally, using time-to-relapse data we identify deoxycholic acid (DCA) as a new prognostic indicator for rUTI recurrence. Together these findings suggest that systemic metabolic processes may influence susceptibility, opening new avenues for therapeutic intervention and the development of more accurate diagnostic and prognostic to improve patient outcomes.

RevDate: 2024-11-01

Pita S, Myers PN, Johansen J, et al (2024)

CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.

Frontiers in microbiology, 15:1425489.

INTRODUCTION: Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites.

METHODS: CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of in silico metagenomes and DNA mock communities.

RESULTS: CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples.

DISCUSSION: Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and is available for a fee at https://cosmosidhub.com.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Chen G, Ren Q, Zhong Z, et al (2024)

Exploring the gut microbiome's role in colorectal cancer: diagnostic and prognostic implications.

Frontiers in immunology, 15:1431747.

The intricate interplay between the gut microbiome and colorectal cancer (CRC) presents novel avenues for early diagnosis and prognosis, crucial for improving patient outcomes. This comprehensive review synthesizes current findings on the gut microbiome's contribution to CRC pathogenesis, highlighting its potential as a biomarker for non-invasive CRC screening strategies. We explore the mechanisms through which the microbiome influences CRC, including its roles in inflammation, metabolism, and immune response modulation. Furthermore, we assess the viability of microbial signatures as predictive tools for CRC prognosis, offering insights into personalized treatment approaches. Our analysis underscores the necessity for advanced metagenomic studies to elucidate the complex microbiome-CRC nexus, aiming to refine diagnostic accuracy and prognostic assessment in clinical settings. This review propels forward the understanding of the microbiome's diagnostic and prognostic capabilities, paving the way for microbiome-based interventions in CRC management.

RevDate: 2024-11-01

Hillege LE, Trepka KR, Ziemons J, et al (2024)

Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients.

medRxiv : the preprint server for health sciences pii:2024.10.11.24315249.

PURPOSE: Unpredictable chemotherapy side effects are a major barrier to successful treatment. Cell culture and mouse experiments indicate that the gut microbiota is influenced by and influences anti-cancer drugs. However, metagenomic data from patients paired to careful side effect monitoring remains limited. Herein, we focus on the oral fluoropyrimidine capecitabine (CAP). We investigate CAP-microbiome interactions through metagenomic sequencing of longitudinal stool sampling from a cohort of advanced colorectal cancer (CRC) patients.

METHODS: We established a prospective cohort study including 56 patients with advanced CRC treated with CAP monotherapy across 4 centers in the Netherlands. Stool samples and clinical questionnaires were collected at baseline, during cycle 3, and post-treatment. Metagenomic sequencing to assess microbial community structure and gene abundance was paired with transposon mutagenesis, targeted gene deletion, and media supplementation experiments. An independent US cohort was used for model validation.

RESULTS: CAP treatment significantly altered gut microbial composition and pathway abundance, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation confirmed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Microbial menaquinol biosynthesis genes were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted hand-foot syndrome and dose reductions in an independent cohort.

CONCLUSION: These results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells, with implications for toxicities outside the gastrointestinal tract. We provide a proof-of-concept for the use of microbiome profiling and machine learning to predict drug toxicities across independent cohorts. These observations provide a foundation for future human intervention studies, more in-depth mechanistic dissection in preclinical models, and extension to other cancer treatments.

RevDate: 2024-10-31
CmpDate: 2024-10-31

Hoffmann A, Hoffmann J, Ruegamer T, et al (2024)

New diagnostic techniques for diagnosing facture-related infections.

Injury, 55 Suppl 6:111898.

The diagnosis of fracture-related infections (FRI) is challenging and requires interdisciplinary efforts. Many diagnostic approaches are based on the algorithms established for prosthetic joint infections (PJI). Data specific to FRI are limited. Microbiological diagnostics include tissue culture, sonication, and molecular methods. Novel metagenomic analyses are increasingly being used in clinical diagnostic practice. In addition to bacterial detection, the study of host tissue factors has the potential to transform the diagnostics of FRI by facilitating the assesment of clinical significance in clinical samples. The integration of host tissue analysis into microbiology reports has great potential to improve the diagnosis of FRI. This mini-review describes the potential improvement of diagnostic techniques by integrating new approaches into the diagnostic algorithm of fracture-related infections.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Although we can't usually see them, microbes are essential for every part of human life—indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying—one at a time—the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )