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Frontiers in Microbiology 2023There are many unidentified microbes in polluted soil needing to be explored and nominated to benefit the study of microbial ecology. In this study, a taxonomic research...
There are many unidentified microbes in polluted soil needing to be explored and nominated to benefit the study of microbial ecology. In this study, a taxonomic research was carried out on five bacterial strains which were isolated and cultivated from polycyclic aromatic hydrocarbons, and heavy metals polluted soil of an abandoned coking plant. Phylogenetical analysis showed that they belonged to the phyla and , and their 16S rRNA gene sequence identities were lower than 98.5% to any known and validly nominated bacterial species, suggesting that they were potentially representing new species. Using polyphasic taxonomic approaches, the five strains were classified as new species of the families and . Genome sizes of the five strains ranged from 3.07 to 6.60 Mb, with overall DNA G+C contents of 63.57-71.22 mol%. The five strains had average nucleotide identity of 72.38-87.38% and digital DNA-DNA hybridization of 14.0-34.2% comparing with their closely related type strains, which were all below the thresholds for species delineation, supporting these five strains as novel species. Based on the phylogenetic, phylogenomic, and phenotypic characterizations, the five novel species are proposed as (type strain H3Y2-19a = CGMCC 1.61332), (type strain H3M29-4 = CGMCC 1.61335T), (type strain H3SJ31-1 = CGMCC 1.61329), (type strain H39-1-10 = CGMCC 1.61325), and (type strain H39-3-25 = CGMCC 1.61326). Comparative genome analysis revealed that the species of the family represented by H39-1-10, H39-3-25, and H3SJ31-1 possessed more functional protein-coding genes for the degradation of aromatic pollutants than the species of the family represented by H3Y2-19a and H3M29-4. Furthermore, their capacities of resisting heavy metals and metabolizing aromatic compounds were investigated. The results indicated that strains H3Y2-19a and H39-3-25 were robustly resistant to chromate (VI) and/or arsenite (III). Strains H39-1-10 and H39-3-25 grew on aromatic compounds, including naphthalene, as carbon sources even in the presence of chromate (VI) and arsenite (III). These features reflected their adaptation to the polluted soil environment.
PubMed: 38088973
DOI: 10.3389/fmicb.2023.1289110 -
Emerging Infectious Diseases May 2024We report a case of Sphingobium yanoikuyae bacteremia in an 89-year-old patient in Japan. No standard antimicrobial regimen has been established for S. yanoikuyae...
We report a case of Sphingobium yanoikuyae bacteremia in an 89-year-old patient in Japan. No standard antimicrobial regimen has been established for S. yanoikuyae infections. However, ceftriaxone and ceftazidime treatments were effective in this case. Increased antimicrobial susceptibility data are needed to establish appropriate treatments for S. yanoikuyae.
Topics: Aged, 80 and over; Humans; Male; Anti-Bacterial Agents; Bacteremia; Gram-Negative Bacterial Infections; Japan; Microbial Sensitivity Tests; Sphingomonadaceae
PubMed: 38666619
DOI: 10.3201/eid3005.231514 -
Frontiers in Microbiology 2023Identification of complex associations between diseases and microbes is important to understand the pathogenesis of diseases and design therapeutic strategies....
INTRODUCTION
Identification of complex associations between diseases and microbes is important to understand the pathogenesis of diseases and design therapeutic strategies. Biomedical experiment-based Microbe-Disease Association (MDA) detection methods are expensive, time-consuming, and laborious.
METHODS
Here, we developed a computational method called SAELGMDA for potential MDA prediction. First, microbe similarity and disease similarity are computed by integrating their functional similarity and Gaussian interaction profile kernel similarity. Second, one microbe-disease pair is presented as a feature vector by combining the microbe and disease similarity matrices. Next, the obtained feature vectors are mapped to a low-dimensional space based on a Sparse AutoEncoder. Finally, unknown microbe-disease pairs are classified based on Light Gradient boosting machine.
RESULTS
The proposed SAELGMDA method was compared with four state-of-the-art MDA methods (MNNMDA, GATMDA, NTSHMDA, and LRLSHMDA) under five-fold cross validations on diseases, microbes, and microbe-disease pairs on the HMDAD and Disbiome databases. The results show that SAELGMDA computed the best accuracy, Matthews correlation coefficient, AUC, and AUPR under the majority of conditions, outperforming the other four MDA prediction models. In particular, SAELGMDA obtained the best AUCs of 0.8358 and 0.9301 under cross validation on diseases, 0.9838 and 0.9293 under cross validation on microbes, and 0.9857 and 0.9358 under cross validation on microbe-disease pairs on the HMDAD and Disbiome databases. Colorectal cancer, inflammatory bowel disease, and lung cancer are diseases that severely threat human health. We used the proposed SAELGMDA method to find possible microbes for the three diseases. The results demonstrate that there are potential associations between and colorectal cancer and one between Sphingomonadaceae and inflammatory bowel disease. In addition, may associate with autism. The inferred MDAs need further validation.
CONCLUSION
We anticipate that the proposed SAELGMDA method contributes to the identification of new MDAs.
PubMed: 37415823
DOI: 10.3389/fmicb.2023.1207209 -
Microbiology Spectrum May 2024Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how...
Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of , a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted clade and functional composition would correspond with site conditions and reflect the composition of native communities. We extracted sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major clades were found at varying relative abundances along the climate gradient, and transplanted clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; < 0.001) on the distribution of both functional (R = 0.465) and clade composition (R = 0.400), suggesting that composition depends on climate parameters. Additionally, for both clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine clade and functional composition.IMPORTANCE is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within , both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.
Topics: Sphingomonas; Climate Change; California; Soil Microbiology; Ecosystem; Phylogeny; Microbiota; Metagenomics; Grassland
PubMed: 38572990
DOI: 10.1128/spectrum.00236-24 -
Scientific Reports Feb 2024Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic...
Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic environments with limited knowledge of their microbial taxonomic composition. In this study, bacterial and archaeal communities of the Obstans Ice Cave (Carnic Alps, Southern Austria) were analyzed by next-generation amplicon sequencing and by cultivation of bacterial strains at 10 °C and studying their metabolism. The most abundant bacterial taxa were uncultured Burkholderiaceae and Brevundimonas spp. in the drip water, Flavobacterium, Alkanindiges and Polaromonas spp. in the ice, Pseudonocardia, Blastocatella spp., uncultured Pyrinomonadaceae and Sphingomonadaceae in carbonate precipitates, and uncultured Gemmatimonadaceae and Longimicrobiaceae in clastic cave sediments. These taxa are psychrotolerant/psychrophilic and chemoorganotrophic bacteria. On a medium with Mg/Ca = 1 at 21 °C and 10 °C, 65% and 35% of the cultivated strains precipitated carbonates, respectively. The first ~ 200 µm-size crystals appeared 2 and 6 weeks after the start of the cultivation experiments at 21 °C and 10 °C, respectively. The crystal structure of these microbially induced carbonate precipitates and their Mg-content are strongly influenced by the Mg/Ca ratio of the culture medium. These results suggest that the high diversity of prokaryotic communities detected in cryogenic subsurface environments actively contributes to carbonate precipitation, despite living at the physical limit of the presence of liquid water.
Topics: Archaea; Bacteria; Calcium Carbonate; Ice; Phylogeny; Extremophiles
PubMed: 38302670
DOI: 10.1038/s41598-024-53131-y -
PloS One 2023Microbes are an important part of the vineyard ecosystem, which significantly influence the quality of grapes. Previously, we identified a bud mutant variety (named...
Microbes are an important part of the vineyard ecosystem, which significantly influence the quality of grapes. Previously, we identified a bud mutant variety (named 'Fengzao') from 'Kyoho' grapes. The variation of microbial communities in grape and its bud mutant variety has not been studied yet. So, in this study, with the samples of both 'Fengzao' and 'Kyoho', we conducted high-throughput microbiome sequencing and investigated their microbial communities in different tissues. Obvious differences were observed in the microbial communities between 'Fengzao' and 'Kyoho'. The fruit and the stem are the tissues with relatively higher abundance of microbes, while the leaves contained less microbes. The fruit and the stem of 'Kyoho' and the stem of 'Fengzao' had relatively higher species diversity based on the alpha diversity analysis. Proteobacteria, Enterobacteriaceae and Rhodobacteraceae had significantly high abundance in 'Fengzao'. Firmicutes and Pseudomonas were highly abundant in the stems of 'Kyoho', and family of Spirochaetaceae, Anaplasmataceae, Chlorobiaceae, and Sphingomonadaceae, and genera of Spirochaeta, Sphingomonas, Chlorobaculum and Wolbachia were abundant in the fruits of 'Kyoho'. These identified microbes are main components of the microbial communities, and could be important regulators of grapevine growth and development. This study revealed the differences in the microbial compositions between 'Kyoho' and its bud mutant, and these identified microbes will be significant resources for the future researches on the quality regulation and disease control of grapevines.
Topics: Chlorobi; Vitis; Microbiota; Anaplasmataceae; Enterobacteriaceae
PubMed: 37647311
DOI: 10.1371/journal.pone.0290853 -
Microorganisms Jun 2023Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for...
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate ( = 24), root ( 24), and fruit ( 24) composite samples were subjected to DNA extraction and high-throughput gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, , , , , , and , were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of , , , , , , , , and . These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.
PubMed: 37512805
DOI: 10.3390/microorganisms11071633 -
Frontiers in Microbiology 2023The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this...
INTRODUCTION
The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.
METHODS
We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.
RESULTS AND DISCUSSION
Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by , , , and , the GL and GLICI communities showed high proportions of and , respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.
PubMed: 38029116
DOI: 10.3389/fmicb.2023.1175663 -
STAR Protocols Sep 2023Paratransgenesis through genetic manipulation of symbiotic or commensal microorganisms has been proposed as an effective and environmentally sound approach for the...
Paratransgenesis through genetic manipulation of symbiotic or commensal microorganisms has been proposed as an effective and environmentally sound approach for the control of vector-borne diseases, including tick bite-related pathologies, and reducing pathogen transmission. Here, we present a protocol for Sphingomonas transformation with Anaplasma phagocytophilum major surface protein 4 and heat shock protein 70. We describe a step-by-step protocol for in vitro study of interactions between transformed Franken Sphingomonas and Ixodes scapularis ISE6 tick cells during A. phagocytophilum infection. For complete details on the use and execution of this protocol, please refer to Mazuecos et al. (2023)..
Topics: Animals; Anaplasma phagocytophilum; Sphingomonas; Coinfection; Ixodes; HSP70 Heat-Shock Proteins
PubMed: 37691149
DOI: 10.1016/j.xpro.2023.102557 -
Applied and Environmental Microbiology Jan 2024The platform chemical muconic acid (MA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate...
The platform chemical muconic acid (MA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates DSM12444 as a chassis for the production of MA from biomass aromatics. The genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to MA. This study confirmed the activity of these two enzymes and compared their activity to ones that have been previously characterized and used in MA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of MA from PCA and produced greater than 100% yield of MA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of MA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in and the genetic tractability of this organism to generate strains that produce MA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of that can be used to produce the commodity chemical -muconic acid from renewable and abundant biomass aromatics.
Topics: Biomass; Sphingomonadaceae; Sorbic Acid; Lignin; Metabolic Engineering; Hydroxybenzoates
PubMed: 38117061
DOI: 10.1128/aem.01660-23