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Nature Food Aug 2023China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the...
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
Topics: Animals; Humans; Anti-Bacterial Agents; Chickens; Drug Resistance, Bacterial; Farms; Metagenomics; Abattoirs; Escherichia coli; Machine Learning
PubMed: 37563495
DOI: 10.1038/s43016-023-00814-w -
Applied Microbiology and Biotechnology Aug 2023The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic...
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr trait is spread across different bacterial taxonomic classes. • The core-code for the Myr trait was detected in a novel ICE, only found in Pseudomonas spp.
Topics: Rhizosphere; Acyclic Monoterpenes; Bacteria; Pseudomonas
PubMed: 37405434
DOI: 10.1007/s00253-023-12650-w -
International Journal of Molecular... Jul 2023Given the impact of the gut microbiome on human physiology and aging, it is possible that the gut microbiome may affect locomotion in the same way as the host's own...
Given the impact of the gut microbiome on human physiology and aging, it is possible that the gut microbiome may affect locomotion in the same way as the host's own genes. There is not yet any direct evidence linking the gut microbiome to locomotion, though there are some potential connections, such as regular physical activity and the immune system. In this study, we demonstrate that the gut microbiome can contribute differently to locomotion. We remodeled the original gut microbiome of mice through fecal microbiota transplantation (FMT) using human feces and compared the changes in locomotion of the same mice before and three months after FMT. We found that FMT affected locomotion in three different ways: positive, none (the same), and negative. Analysis of the phylogenesis, α-diversities, and β-diversities of the gut microbiome in the three groups showed that a more diverse group of intestinal microbes was established after FMT in each of the three groups, indicating that the human gut microbiome is more diverse than that of mice. The FMT-remodeled gut microbiome in each group was also different from each other. Fold change and linear correlation analyses identified , , and in the gut microbiome as positive contributors to locomotion, while , , , and were found to have negative effects. This study not only confirms the presence of gut microbiomes that contribute differently to locomotion, but also explains the mixed results in research on the association between the gut microbiome and locomotion.
Topics: Humans; Animals; Mice; Fecal Microbiota Transplantation; Feces; Gastrointestinal Microbiome; Microbiota; Locomotion
PubMed: 37511151
DOI: 10.3390/ijms241411392 -
Applied Microbiology and Biotechnology Sep 2023Pharmaceuticals are of concern to our planet and health as they can accumulate in the environment. The impact of these biologically active compounds on ecosystems is...
Pharmaceuticals are of concern to our planet and health as they can accumulate in the environment. The impact of these biologically active compounds on ecosystems is hard to predict, and information on their biodegradation is necessary to establish sound risk assessment. Microbial communities are promising candidates for the biodegradation of pharmaceuticals such as ibuprofen, but little is known yet about their degradation capacity of multiple micropollutants at higher concentrations (100 mg/L). In this work, microbial communities were cultivated in lab-scale membrane bioreactors (MBRs) exposed to increasing concentrations of a mixture of six micropollutants (ibuprofen, diclofenac, enalapril, caffeine, atenolol, paracetamol). Key players of biodegradation were identified using a combinatorial approach of 16S rRNA sequencing and analytics. Microbial community structure changed with increasing pharmaceutical intake (from 1 to 100 mg/L) and reached a steady-state during incubation for 7 weeks on 100 mg/L. HPLC analysis revealed a fluctuating but significant degradation (30-100%) of five pollutants (caffeine, paracetamol, ibuprofen, atenolol, enalapril) by an established and stable microbial community mainly composed of Achromobacter, Cupriavidus, Pseudomonas and Leucobacter. By using the microbial community from MBR1 as inoculum for further batch culture experiments on single micropollutants (400 mg/L substrate, respectively), different active microbial consortia were obtained for each single micropollutant. Microbial genera potentially responsible for degradation of the respective micropollutant were identified, i.e. Pseudomonas sp. and Sphingobacterium sp. for ibuprofen, caffeine and paracetamol, Sphingomonas sp. for atenolol and Klebsiella sp. for enalapril. Our study demonstrates the feasibility of cultivating stable microbial communities capable of degrading simultaneously a mixture of highly concentrated pharmaceuticals in lab-scale MBRs and the identification of microbial genera potentially responsible for the degradation of specific pollutants. KEY POINTS: • Multiple pharmaceuticals were removed by stable microbial communities. • Microbial key players of five main pharmaceuticals were identified.
Topics: Ibuprofen; RNA, Ribosomal, 16S; Atenolol; Acetaminophen; Caffeine; Microbiota; Bioreactors; Biodegradation, Environmental; Environmental Pollutants; Water Pollutants, Chemical; Pharmaceutical Preparations
PubMed: 37436483
DOI: 10.1007/s00253-023-12677-z -
Plant Disease Apr 2024Cauliflower mushroom (Sparassis latifolia), is widely distributed in Australia, North America, Europe, and East Asia (Bashir et al., 2020). It is known for its medicinal...
Cauliflower mushroom (Sparassis latifolia), is widely distributed in Australia, North America, Europe, and East Asia (Bashir et al., 2020). It is known for its medicinal significance due to the availability of various pharmacological substances and their use in health supplements (Bashir et al., 2017). In recent years, with the development of artificial cultivation technology, S. latifolia has been industrialized in China, with an annual output value 50 million dollars. In March 2023, approximately 15% of S. latifolia showed obvious bacterial rot in mushroom hothouse (about 0.05 ha), located in Shuangliu county, Sichuan province, China (104°7'51"N, 30°25'2"E). The affected parts appear water-soaked, and become sunken and softened as the disease progresses. In the finally, all the fruiting body tissues turn into paste, with colors pale yellow, and have a foul smell. The pathogen was isolated from the margin of the lesions by dilution and streaking techniques onto Nutrient Agar, and incubated at 28℃ in the dark for 2-3 days. A single colony was re-streak for purification. Eight isolates were obtained from five samples collected randomly. The representative three isolates were selected for further characterization. For pathogenicity testing, ten health fruit bodies of S. latifolia were selected (for per isolate). Bacterial suspensions (1 × 107 CFU/ml) of the three isolates were applied to the fruiting body until wet, sterile water was used as controls. All the S. latifolia were maintained at 19±1℃, 85-100% relative humidity, and 18 h of light in the mushroom hothouse. Three days later, the inoculated fruiting bodies developed yellow color, and appear water-soaked, five days later, fruiting body gradually turn to soft and part turn to rot, seven days later, the fruiting body tissues completely turn into paste with a foul smell. The symptoms exhibited were similar to those of the original diseased fruiting bodies, while the control group remained healthy. The same bacterial were re-isolated from the infected fruiting bodies and subsequently identified by morphological characteristics and DNA sequenced. The pathogenicity test was conducted three times, each yielding similar results. The colonies of the pathogen are gram-negative rods, medium sized, convex, smooth, opaque, turning yellow after several days at a temperature 28℃. For molecular identification, the DNA of the representative three isolates was extracted using a Bacterial Genomic DNA Extraction Kit (Solarbio, Beijing). The 16S rRNA genes were amplified and sequenced with the primer 27F/1492R (Lane et al., 1985). Finally, the sequences were identical. The generated representative sequence was deposited in GenBank with accession number OR399122. BLASTn analysis showed 100% identity (1404/1404 bp) with previously deposited sequence (accession number CP068224) of S. multivorum FDAARGOS in GenBank. Based on the maximum likelihood method, phylogenetic analysis revealed 100% bootstrap support values with S. multivorum. Finally, the bacterium was identified as S. multivorum. This is the first report of S. multivorum causing bacterial rot of mushroom. The fruiting body of S. multivorum consists of multiple folded flat lobes, which are thin and have large surface area, may facilitate the infection of S. multivorum. Sphingobacterium sp. are named for their synthesize sphingolipids, which play an important role in bacterial infection (Kunz et al., 2019). These results will contribute to developing control strategies for this disease.
PubMed: 38587796
DOI: 10.1094/PDIS-01-24-0022-PDN -
Pathogens (Basel, Switzerland) Oct 2023This study was conducted to investigate the antagonistic potential of endophytic and rhizospheric bacterial isolates obtained from in suppressing and and promoting...
This study was conducted to investigate the antagonistic potential of endophytic and rhizospheric bacterial isolates obtained from in suppressing and and promoting the growth of cucumber. Molecular identification of bacterial strains associated with confirmed that these strains belong to the , , , , , , , , , and genera. A dual culture assay showed that nine of the bacterial strains exhibited antifungal activity, four of which were effective against both pathogens. Strains B27 () and B28 () caused the highest percentage of inhibition towards (48.5% and 48.1%, respectively). growth was impeded by the B21 (, 44.7%) and B28 (, 51.1%) strains. Scanning electron microscopy showed that the strains caused abnormality in phytopathogens' mycelia. All of the selected bacterial strains showed good IAA production (>500 ppm). A paper towel experiment demonstrated that these strains improved the seed germination, root/shoot growth, and vigor index of cucumber seedlings. Our findings suggest that the bacterial strains from are suppressive to and and can promote cucumber growth. This appears to be the first study to report the efficacy of these bacterial strains from against and .
PubMed: 38003740
DOI: 10.3390/pathogens12111275 -
Microorganisms Apr 2024Carbapenems are last-resort antibiotics used to treat multidrug-resistant bacterial infections. Resistance to carbapenems has been designated as an urgent threat and is...
Carbapenems are last-resort antibiotics used to treat multidrug-resistant bacterial infections. Resistance to carbapenems has been designated as an urgent threat and is increasing in healthcare settings. However, little is still known about the distribution and characteristics of carbapenem-resistant bacteria (CRB) outside of healthcare settings. Here, we surveyed the distribution of CRB in ten diverse freshwater and seawater environments in California, U.S., ranging from San Luis Obispo County to San Bernardino County, combining both direct isolation and enrichment approaches to increase the diversity of isolated CRB. From the locations surveyed, we selected 30 CRB for further characterization. These isolates were identified as members of the genera , , , , , , and . These isolates were resistant to carbapenems, other β-lactams, and often to other antibiotics (tetracycline, gentamicin, or ciprofloxacin). We also found that nine isolates belonging to the genera , (), and () produced carbapenemases. Overall, our findings indicate that sampling different types of aquatic environments and combining different isolation approaches increase the diversity of the environmental CRB obtained. Moreover, our study supports the increasingly recognized role of natural water systems as an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including bacteria carrying carbapenemase genes.
PubMed: 38674746
DOI: 10.3390/microorganisms12040802 -
Environment International Aug 2023The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing...
The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing accumulation of secondary pollutants in soils. The decomposition of PE film-sourced pollutants is directly associated with the enrichment of specific bacterial communities. We therefore hypothesized that plant biomass may act as an organic media to mediate the pollutant decomposition via reshaping bacterial communities. To validate this hypothesis, plant biomass (dried maize straw and living clover) was embedded at the underlying surface of PE film, to track the changes in the composition and function of bacterial communities in maize field across two years. The results indicated that both dry crop straw and alive clover massively promoted the α-diversity and abundance of dominant bacteria at plastisphere, relative to bulk soil. Bacterial communities tended to be clustered at plastisphere, forming the bacteria islands to enrich pollutant-degrading bacteria, such as Sphingobacterium, Arthrobacter and Paracoccus. As such, plastisphere bacteria islands substantially enhanced the degradation potential of chloroalkene and benzoate (p < 0.05). Simultaneously, bacterial network became stabilized and congregated at plastisphere, and markedly improved the abundance of plastisphere module hubs and connectors bacteria via stochastic process. Particularly, bacterial community composition and plastic film-sourced pollutants metabolism were evidently affected by soil pH, carbon and nitrogen sources that were mainly derived from the embedded biomass. To sum up, plant biomass embedding as a nature-based strategy (NbS) can positively mediate the decomposition of plastic-sourced pollutants through plastisphere bacteria island effects.
Topics: Soil; Biomass; Polyethylene; Environmental Pollutants; Water; Agriculture; Plastics; Bacteria; Soil Microbiology
PubMed: 37499460
DOI: 10.1016/j.envint.2023.108114 -
Journal of Environmental Management Jan 2024Bioactive coatings are envisaged as a promising biotechnology to tackle the emerging problem of indoor air pollution. This solution could cope with the low...
Bioactive coatings are envisaged as a promising biotechnology to tackle the emerging problem of indoor air pollution. This solution could cope with the low concentrations, the wide range of compounds and the hydrophobicity of some indoor air VOCs, which are the most important bottlenecks regarding the implementation of conventional biotechnologies for indoor air treatment. A bioactive coating-based bioreactor was tested in this study for the abatement of different VOCs (n-hexane, toluene and α-pinene) at different empty bed residence times (EBRT) and inlet VOC concentrations. The performance of this reactor was compared with a conventional biofilm-based bioreactor operated with the same microbial inoculum. After an acclimation period, the bioactive coating-based bioreactor achieved abatements of over 50% for hexane, 80% for toluene and 70% for pinene at EBRTs of 112-56 s and inlet concentrations of 9-15 mg m. These results were about 25, 10 and 20% lower than the highest removals recorded in the biofilm-based bioreactor. Both bioreactors experienced a decrease in VOC abatement by ∼25% for hexane, 45% for toluene and 40% for pinene, after reducing the EBRT to 28 s. When inlet VOC concentrations were progressively reduced, VOC abatement efficiencies did not improve. This fact suggested that low EBRTs and low inlet VOCs concentration hindered indoor air pollutant abatement as a result of a limited mass transfer and bioavailability. Metagenomic analyses showed that process operation with toluene, hexane and pinene as the only carbon and energy sources favored an enriched bacterial community represented by the genera Devosia, Mesorhizobium, Sphingobacterium and Mycobacterium, regardless of the bioreactor configuration. Bioactive coatings were used in this work as packing material of a conventional bioreactor, achieving satisfactory VOC abatement similar to a conventional bioreactor.
Topics: Air Pollution, Indoor; Hexanes; Volatile Organic Compounds; Air Pollutants; Bioreactors; Toluene; Filtration
PubMed: 37897901
DOI: 10.1016/j.jenvman.2023.119362 -
BMC Microbiology Jul 2023It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or...
BACKGROUND
It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or exacerbation. Co-occurrence networks have been widely adopted to identify biomarkers and keystone taxa in the pathogenesis of microbiome-related diseases. Despite the promising results that network-driven approaches have led to in various human diseases, there is a dearth of research pertaining to key taxa that contribute to the pathogenesis of lung cancer. Therefore, our primary goal in this study is to explore co-existing relationships among members of the lung microbial community and any potential gained or lost interactions in lung cancer.
RESULTS
Using integrative and network-based approaches, we integrated four studies assessing the microbiome of lung biopsies of cancer patients. Differential abundance analyses showed that several bacterial taxa are different between tumor and tumor-adjacent normal tissues (FDR adjusted p-value < 0.05). Four, fifteen, and twelve significantly different associations were found at phylum, family, and genus levels. Diversity analyses suggested reduced alpha diversity in the tumor microbiome. However, beta diversity analysis did not show any discernible pattern between groups. In addition, four distinct modules of bacterial families were detected by the DBSCAN clustering method. Finally, in the co-occurrence network context, Actinobacteria, Firmicutes, Bacteroidetes, and Chloroflexi at the phylum level and Bifidobacterium, Massilia, Sphingobacterium, and Ochrobactrum at the genus level showed the highest degree of rewiring.
CONCLUSIONS
Despite the absence of statistically significant differences in the relative abundance of certain taxa between groups, it is imperative not to overlook them for further exploration. This is because they may hold pivotal central roles in the broader network of bacterial taxa (e.g., Bifidobacterium and Massilia). These findings emphasize the importance of a network analysis approach for studying the lung microbiome since it could facilitate identifying key microbial taxa in lung cancer pathogenesis. Relying exclusively on differentially abundant taxa may not be enough to fully grasp the complex interplay between lung cancer and the microbiome. Therefore, a network-based approach can offer deeper insights and a more comprehensive understanding of the underlying mechanisms.
Topics: Humans; Carcinoma, Non-Small-Cell Lung; Lung Neoplasms; Actinobacteria; Bifidobacterium; Microbiota; Lung
PubMed: 37434142
DOI: 10.1186/s12866-023-02931-9