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Oncogene Jul 2022The consistency of the associations between gastric mucosal microbiome and gastric cancer across studies remained unexamined. We aimed to identify universal microbial... (Meta-Analysis)
Meta-Analysis
The consistency of the associations between gastric mucosal microbiome and gastric cancer across studies remained unexamined. We aimed to identify universal microbial signatures in gastric carcinogenesis through a meta-analysis of gastric microbiome from multiple studies. Compositional and ecological profiles of gastric microbes across stages of gastric carcinogenesis were significantly altered. Meta-analysis revealed that opportunistic pathobionts Fusobacterium, Parvimonas, Veillonella, Prevotella and Peptostreptococcus were enriched in GC, while commensals Bifidobacterium, Bacillus and Blautia were depleted in comparison to SG. The co-occurring correlation strengths of GC-enriched bacteria were increased along disease progression while those of GC-depleted bacteria were decreased. Eight bacterial taxa, including Veillonella, Dialister, Granulicatella, Herbaspirillum, Comamonas, Chryseobacterium, Shewanella and Helicobacter, were newly identified by this study as universal biomarkers for robustly discriminating GC from SG, with an area under the curve (AUC) of 0.85. Moreover, H. pylori-positive samples exhibited reduced microbial diversity, altered microbiota community and weaker interactions among gastric microbes. Our meta-analysis demonstrated comprehensive and generalizable gastric mucosa microbial features associated with histological stages of gastric carcinogenesis, including GC associated bacteria, diagnostic biomarkers, bacterial network alteration and H. pylori influence.
Topics: Carcinogenesis; Dysbiosis; Gastric Mucosa; Helicobacter Infections; Helicobacter pylori; Humans; Microbiota; Stomach; Stomach Neoplasms
PubMed: 35680985
DOI: 10.1038/s41388-022-02377-9 -
Journal of Experimental Botany Sep 2022Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and...
Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25-30 plants h-1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH4NO3 the benefit appears through N fixation, while at 0.5 mM NH4NO3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.
Topics: Ammonium Compounds; Brachypodium; Ecosystem; Edible Grain; Herbaspirillum; Nitrates; Plant Roots
PubMed: 35512445
DOI: 10.1093/jxb/erac184 -
World Journal of Microbiology &... May 2022Linear alkyl sulfates are a major class of surfactants that have large-scale industrial application and thus wide environmental release. These organic pollutants...
Linear alkyl sulfates are a major class of surfactants that have large-scale industrial application and thus wide environmental release. These organic pollutants threaten aquatic environments and other environmental compartments. We show the promise of the use of a whole-cell electric sensor in the analysis of low or residual concentrations of sodium dodecyl sulfate (SDS) in aqueous solutions. On the basis of bioinformatic analysis and alkylsulfatase activity determinations, we chose the gram-negative bacterium Herbaspirillum lusitanum, strain P6-12, as the sensing element. Strain P6-12 could utilize 0.01-400 mg/L of SDS as a growth substrate. The electric polarizability of cell suspensions changed at all frequencies used (50-3000 kHz). The determination limit of 0.01 mg/L is much lower than the official requirements for the content of SDS in potable and process water (0.5 and 1.0 mg/L, respectively), and the analysis takes about 1-5 min. The promise of H. lusitanum P6-12 for use in the remediation of SDS-polluted soils is discussed.
Topics: Environmental Pollution; Sodium Dodecyl Sulfate; Sulfates; Surface-Active Agents
PubMed: 35614280
DOI: 10.1007/s11274-022-03309-1 -
Revista Chilena de Infectologia :... 2018
Topics: Herbaspirillum
PubMed: 30725001
DOI: 10.4067/s0716-10182018000500545 -
Frontiers in Microbiology 2022Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated...
Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., , Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.
PubMed: 35602076
DOI: 10.3389/fmicb.2022.888086 -
Plants (Basel, Switzerland) Dec 2022is an endophytic bacterium that can fix nitrogen and synthesize phytohormones, which can lead to a plant growth-promoting effect when used as a microbial inoculant....
is an endophytic bacterium that can fix nitrogen and synthesize phytohormones, which can lead to a plant growth-promoting effect when used as a microbial inoculant. Studies focused on mechanisms of action are crucial for a better understanding of the bacteria-plant interaction and optimization of plant growth-promoting response. This work aims to understand the underlined mechanisms responsible for the early stimulatory growth effects of inoculation in maize. To perform these studies, we combined transcriptomic and proteomic approaches with physiological analysis. The results obtained eight days after inoculation (d.a.i) showed increased root biomass (233 and 253%) and shoot biomass (249 and 264%), respectively, for the fresh and dry mass of maize-inoculated seedlings and increased green content and development. Omics data analysis, before a positive biostimulation phenotype (5 d.a.i.) revealed that inoculation increases N-uptake and N-assimilation machinery through differentially expressed nitrate transporters and amino acid pathways, as well carbon/nitrogen metabolism integration by the tricarboxylic acid cycle and the polyamine pathway. Additionally, phytohormone levels of root and shoot tissues increased in bacterium-inoculated-maize plants, leading to feedback regulation by the ubiquitin-proteasome system. The early biostimulatory effect of partially results from hormonal modulation coupled with efficient nutrient uptake-assimilation and a boost in primary anabolic metabolism of carbon-nitrogen integrative pathways.
PubMed: 36616175
DOI: 10.3390/plants12010048 -
Diseases of Aquatic Organisms Dec 2022The Critically Endangered southern corroboree frog Pseudophryne corroboree is dependent upon captive assurance colonies for its continued survival. Although the captive...
The Critically Endangered southern corroboree frog Pseudophryne corroboree is dependent upon captive assurance colonies for its continued survival. Although the captive breeding programme for this species has largely been successful, embryonic mortality remains high (40-90% per year). This study aimed to investigate the causes of mortality in P. corroboree embryos in the captive collection at Melbourne Zoo. During the 2021 breeding season, we investigated 108 abnormal embryos to determine the impact of infections and anatomical deformities on survival and used culture and molecular methods to identify microbes. Overall, 100% of abnormal embryos had fungal infections, and of these, 41.6% also had anatomical deformities. The mortality rate in abnormal embryos was 89.8%; however, we detected no difference in survival in any of the 3 observed fungal growth patterns or between deformed and non-deformed embryos. Sanger sequencing of the ITS region identified fungal isolates belonging to the genus Ilyonectria, the first record in a vertebrate host, and another as a Plectosphaerella sp., which is the first record of infection in an embryo. Dominant bacteria identified were of the genera Herbaspirillum and Flavobacterium; however, their role in the mortality is unknown. Fungal infection and deformities have a significant impact on embryo survival in captive-bred P. corroboree. In a species which relies on captive breeding, identifying and reducing the impacts of embryonic mortality can inform conservation efforts and improve reintroduction outcomes.
Topics: Animals; Anura; Seasons; Flavobacterium
PubMed: 36453456
DOI: 10.3354/dao03706 -
BMC Microbiology Oct 2022Azolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have...
BACKGROUND
Azolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have presented that Azolla harbors diverse bacteria that may play a key role in host fitness and productivity. However, the characteristics of endophytic bacteria inhabiting the phyllosphere of different species of Azolla have not yet been fully understood.
RESULTS
In this study, the 16S ribosomal DNA (rDNA) V5-V7 region of bacteria was determined by Illumina high-throughput sequencing platform to study the diversity and richness of endophytic bacterial communities in the phyllosphere of five Azolla species collected from different countries. A total of 1150 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. According to the α diversity indices, the diversity of bacteria was ordered as Azolla imbricata > A. pinnata > A. filiculoides > A. mexicana > A. caroliniana. The PCoA results displayed that the bacterial communities of A. mexicana and A. caroliniana shared the highest similarity, followed by the similarity between A. pinnata and A. imbricata, and they were significantly distinct from the community of A. filiculoides. The dominant bacteria of Azolla mainly belonged to the phylum of Proteobacteria, followed by Actinobacteria, Chlorobillobacteria, and Firmicutes. In detail, the relative abundance of Proteobacteria in A. imbricata was 52.23%, whereas it was more than 80.00% in the other four species of Azolla. Notably, Herbaspirillum (45.91%, 44.08%) and Methylophilus (29.97%, 37.96%) were the main genera inhabiting A. mexicana and A. caroliniana respectively. Ferrovibrio (18.54%) and Rhizobium (16.68%) were the dominant genera inhabiting A. filiculoides. The group of unidentified genera (41.63%, 44.92%) consisted most of the bacteria in A. imbricata and A. pinnata respectively. Further analysis suggested that the significant different bacteria identified in LDA Effect Size analysis existed Azolla species-specific patterns.
CONCLUSIONS
In summary, all results suggested that the diversity and composition of the endophytic bacterial communities were different in Azolla species.
Topics: Cyanobacteria; DNA, Ribosomal; Ecosystem; Ferns; High-Throughput Nucleotide Sequencing; Nitrogen; Proteobacteria; RNA, Ribosomal, 16S
PubMed: 36221067
DOI: 10.1186/s12866-022-02639-2 -
Microorganisms May 2020Bacteria from the genera and can promote the growth of , but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized...
Bacteria from the genera and can promote the growth of , but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with strain IAC/BECa 135 and strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with strain IAC/BECa 135 than in those inoculated with strain IAC/BECa 152. Conversely, plants inoculated with strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.
PubMed: 32414048
DOI: 10.3390/microorganisms8050725 -
Cureus Mar 2023The species are gram-negative bacteria that inhabit soil and water. Infections caused by this pathogen are an uncommon clinical entity. We describe a rare case of...
The species are gram-negative bacteria that inhabit soil and water. Infections caused by this pathogen are an uncommon clinical entity. We describe a rare case of septic shock and bacteremia caused by in an immunocompetent adult female. The patient, a 59-year-old female, presented to the hospital with circulatory shock, fever, chills, and cough. Chest x-ray revealed right lower lobe lung consolidation consistent with pneumonia, and blood cultures with a positive concerning gram-negative curved rod which was later identified as . The patient was treated in the ICU for three days with cefepime and vasoactive agents. After improvement and an additional seven days of hospitalization, the patient was discharged home with a five-day course of oral levofloxacin. Although our patient responded well to cefepime and levofloxacin, meropenem and piperacillin-tazobactam were found to be the most commonly used and the most effective antibiotics to treat infections in other reported cases. This is amongst the few reported cases of bacteremia in an immunocompetent individual with pneumonia.
PubMed: 37065293
DOI: 10.7759/cureus.36155