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ISME Communications Sep 2023Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an...
Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.
PubMed: 37660098
DOI: 10.1038/s43705-023-00302-z -
BMC Microbiology Aug 2023Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with...
Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.
BACKGROUND
Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.
RESULTS
Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MIC (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.
CONCLUSIONS
Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.
Topics: Arsenic; Arsenites; Phylogeny; Microbiota
PubMed: 37648982
DOI: 10.1186/s12866-023-02980-0 -
Frontiers in Plant Science 2023Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses...
Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. is a unique perennial wild rice species in China with rich genetic resources. However, endophytic bacterial communities of this species and their plant growth-promoting (PGP) traits remain largely unknown. In this study, endophytic bacteria in the root, stem, and leaf tissues of were characterized using 16S rRNA gene Illumina sequencing. Culturable bacterial endophytes were also isolated from . tissues and characterized for their PGP traits. The microbiome analysis showed a more complex structure and powerful function of the endophytic bacterial community in roots compared with those in other tissue compartments. Each compartment had its specific endophytic bacterial biomarkers, including and for roots; and for stems; and , , and for leaves. A total of 96 endophytic bacterial strains with PGP traits of phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, and siderophore or indole-3-acetic acid (IAA) production were isolated from . Among them, 11 strains identified as , . , . , , . , and were selected for inoculation of perennial rice based on their IAA production traits. These strains showed promising PGP effects on perennial rice seedlings. They promoted plants to form a strong root system, stimulate biomass accumulation, and increase chlorophyll content and nitrogen uptake, which could fulfil the ecologically sustainable cultivation model of perennial rice. These results provide insights into the bacterial endosphere of and its application potential in perennial rice. There is the prospect of mining beneficial endophytic bacteria from wild rice species, which could rewild the microbiome of cultivated rice varieties and promote their growth.
PubMed: 37645460
DOI: 10.3389/fpls.2023.1184489 -
Frontiers in Plant Science 2023In recent years, the problem of Cd pollution in paddy fields has become more and more serious, which seriously threatens the safe production of food crops and human...
In recent years, the problem of Cd pollution in paddy fields has become more and more serious, which seriously threatens the safe production of food crops and human health. Using microorganisms to reduce cadmium pollution in rice fields is a green, safe and efficient method, the complicated interactions between the microbes in rice roots throughout the process of cadmium absorption by rice roots are poorly understood. In this investigation, a hydroponic pot experiment was used to examine the effects of bacteria R3 ( sp) and T4 () on cadmium uptake and the endophytic bacterial community in rice roots. The results showed that compared with CK (Uninoculated bacterial liquid), the two strains had significant inhibitory or promotive effects on cadmium uptake in rice plant, respectively. Among them, the decrease of cadmium content in rice plants by R3 strain reached 78.57-79.39%, and the increase of cadmium content in rice plants by T4 strain reached 140.49-158.19%. Further investigation showed that the cadmium content and root cadmium enrichment coefficient of rice plants were significantly negatively correlated with the relative abundances of and , and significantly positively correlated with the relative abundances of , and . Moreover, a more complex network of microbes in rice roots inhibited rice plants from absorbing cadmium. These results suggest that cadmium uptake by rice plants is closely related to the endophytic bacterial community of roots. This study provides a reference scheme for the safe production of crops in cadmium contaminated paddies and lays a solid theoretical foundation for subsequent field applications.
PubMed: 37636120
DOI: 10.3389/fpls.2023.1196130 -
Viruses Jul 2023species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by CF418 or CF116 experienced...
species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by CF418 or CF116 experienced fatal exacerbations. spp. are naturally resistant to several antibiotics. Therefore, phages could be valuable as therapeutics for the control of . In this study, thirteen lytic phages were isolated and characterized at the morphological and genomic levels for potential future use in phage therapy. They are presented here as the Kumeyaay phage collection. Six distinct phage genome clusters were identified based on a comprehensive phylogenetic analysis of the Kumeyaay collection as well as the publicly available phages. The infectivity of all phages in the Kumeyaay collection was tested in 23 clinical isolates; 78% of these isolates were lysed by at least one phage. A cryptic prophage was induced in CF418 when infected with some of the lytic phages. This prophage genome was characterized and is presented as phage CF418-P1. Prophage induction during lytic phage preparation for therapy interventions require further exploration. Large-scale production of phages and removal of endotoxins using an octanol-based procedure resulted in a phage concentrate of 1 × 10 plaque-forming units per milliliter with an endotoxin concentration of 65 endotoxin units per milliliter, which is below the Food and Drugs Administration recommended maximum threshold for human administration. This study provides a comprehensive framework for the isolation, bioinformatic characterization, and safe production of phages to kill spp. in order to potentially manage Cystic Fibrosis (CF) pulmonary infections.
Topics: Adult; Humans; Bacteriophages; Cystic Fibrosis; Phylogeny; Achromobacter; Achromobacter denitrificans; Prophages; Endotoxins
PubMed: 37632008
DOI: 10.3390/v15081665 -
Molecules (Basel, Switzerland) Aug 2023Coffee fermentation is crucial for flavor and aroma, as microorganisms degrade mucilage and produce metabolites. This study aimed to provide a basis for understanding...
Coffee fermentation is crucial for flavor and aroma, as microorganisms degrade mucilage and produce metabolites. This study aimed to provide a basis for understanding the impact of microorganisms on from Yunnan, China, during washed processing. The microbial community structure and differentially changed metabolites (DCMs) of beans during washed processing were analyzed. The results indicated that the top five predominant microorganisms at the genera level were , , , , and for bacteria and , , , , and for fungi. Meanwhile, the relative content of 115 DCMs in 36 h samples decreased significantly, compared to non-fermentation coffee samples (VIP > 1, < 0.05, FC < 0.65), and the relative content of 28 DCMs increased significantly (VIP > 1, < 0.05, FC > 1.5). Furthermore, 17 DCMs showed a strong positive correlation with microorganisms, and 5 DCMs had a strong negative correlation ( < 0.05, |r| > 0.6). Therefore, the interaction and metabolic function of microbiota play a key role in the formation of coffee flavor, and these results help in clarifying the fermentation mechanisms of and in controlling and improving the quality of coffee flavor.
Topics: Coffea; Coffee; China; Fermentation; Microbiota; Saccharomycetales
PubMed: 37630344
DOI: 10.3390/molecules28166092 -
International Journal of Applied &... 2023causes opportunistic nosocomial infections in immunocompromised patients with high mortality. It is underreported as it is often misidentified by conventional...
BACKGROUND
causes opportunistic nosocomial infections in immunocompromised patients with high mortality. It is underreported as it is often misidentified by conventional microbiological methods.
AIMS
The aim of the study is to access the clinicomicrobiological profile and antibiogram of . from clinical isolates.
MATERIALS AND METHODS
It is an observational study done from July 2020 to December 2021 in our hospital. All nonduplicate isolates of from blood and respiratory samples were initially identified with VITEK-2 GN card system and further confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Antibiogram and treatment outcomes were also studied.
RESULTS
. was isolated from 14 patients. Blood samples yielded most isolates (71.4%; = 10) followed by tracheal aspirate and bronchoalveolar lavage fluid. Bacteremia followed by pneumonia was the most common clinical manifestation of infection. All the isolates were identified as . and showed 100% susceptibility to minocycline and piperacillin-tazobactam. Diabetes mellitus and malignancy were the most common underlying condition in these patients. A favorable outcome was seen in 78.6% of the individuals with timely institution of antibiotics and proper diagnosis.
CONCLUSION
Infections due to are on the rise in developing countries like India. Resistance to many classes of antimicrobials makes its treatment more challenging therefore it should always be guided by antibiograms. The present study highlights the significance of this rare bacterium in patients with malignancies in India and advocates greater vigilance toward appropriate identification of this organism.
PubMed: 37614834
DOI: 10.4103/ijabmr.ijabmr_520_22 -
Cureus Jul 2023, also known as , is a low-virulence, non-fermenter gram-negative bacillus mainly found in marine environments. We report a detailed series of four high-risk cases of...
, also known as , is a low-virulence, non-fermenter gram-negative bacillus mainly found in marine environments. We report a detailed series of four high-risk cases of septicemia with the common variable of positive blood cultures for . All four blood isolates were multi-drug resistant and susceptible to meropenem and trimethoprim-sulfamethoxazole. Two patients responded well to the treatment with meropenem and trimethoprim-sulfamethoxazole and two patients died. It should never be assumed that is a contaminant even though it is relatively infrequently isolated from clinical samples. This infection can progress to fatal bacteremia, even in otherwise healthy people, and it can potentially cause severe conditions in premature infants. With only a limited number of antibiotics demonstrating bactericidal properties, the possibility of failure in empirical treatment is significant. As a result, it is important to have a precise comprehension of this uncommon yet deadly illness in order to increase the probability of successful treatment.
PubMed: 37602012
DOI: 10.7759/cureus.42052 -
Cell Reports Aug 2023How the opportunistic Gram-negative pathogens of the genus Achromobacter interact with the innate immune system is poorly understood. Using three Achromobacter clinical...
How the opportunistic Gram-negative pathogens of the genus Achromobacter interact with the innate immune system is poorly understood. Using three Achromobacter clinical isolates from two species, we show that the type 3 secretion system (T3SS) is required to induce cell death in human macrophages by inflammasome-dependent pyroptosis. Macrophages deficient in the inflammasome sensors NLRC4 or NLRP3 undergo pyroptosis upon bacterial internalization, but those deficient in both NLRC4 and NLRP3 do not, suggesting either sensor mediates pyroptosis in a T3SS-dependent manner. Detailed analysis of the intracellular trafficking of one isolate indicates that the intracellular bacteria reside in a late phagolysosome. Using an intranasal mouse infection model, we observe that Achromobacter damages lung structure and causes severe illness, contingent on a functional T3SS. Together, we demonstrate that Achromobacter species can survive phagocytosis by promoting macrophage cell death and inflammation by redundant mechanisms of pyroptosis induction in a T3SS-dependent manner.
Topics: Humans; Animals; Mice; Pyroptosis; Inflammasomes; NLR Family, Pyrin Domain-Containing 3 Protein; Type III Secretion Systems; Achromobacter; Disease Models, Animal; Calcium-Binding Proteins; CARD Signaling Adaptor Proteins
PubMed: 37598340
DOI: 10.1016/j.celrep.2023.113012 -
Molecular Plant-microbe Interactions :... Jul 2023
Topics: Vitis; Xylella; Plant Diseases
PubMed: 37578833
DOI: 10.1094/MPMI-08-22-0169-A