-
Frontiers in Microbiology 2021Four strains belonging to the family of were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three...
Four strains belonging to the family of were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as . The sequence similarity of these three ISS strains, designated as IF7SW-B2, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gene, with the closest being SE2.11. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble and since they assimilate similar sugars as sole carbon substrate when compared to other species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C -ω7 and C -ω6. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus , and the name sp. nov. is proposed. The type strain is IF7SW-B2 (NRRL B-65601 and LMG 32165).
PubMed: 33790880
DOI: 10.3389/fmicb.2021.639396 -
New Microbes and New Infections Mar 2021In 2019, by culturing a skin swab from the forehead of a 70-year-old healthy woman via the culturomics method, we isolated the new bacterial strain Marseille-Q2068T (=...
In 2019, by culturing a skin swab from the forehead of a 70-year-old healthy woman via the culturomics method, we isolated the new bacterial strain Marseille-Q2068T (= CSUR-Q2068). Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S ribosomal RNA gene and genome-to-genome comparison suggested that this taxon belongs to a novel bacterial species within the family in the phylum Proteobacteria. We describe here its main phenotypic characteristics, genome sequence and annotation of strain Marseille-Q2068T, a new member of the genus, which we propose as the type strain.
PubMed: 33659063
DOI: 10.1016/j.nmni.2021.100839 -
PloS One 2021Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this...
Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.
Topics: Archaea; Bacteria; Gene Expression Profiling; Microbiota; Oryza; Phylogeny; Plant Leaves; Plant Roots; RNA, Ribosomal, 16S; Rhizome
PubMed: 33556120
DOI: 10.1371/journal.pone.0246687 -
International Journal of Environmental... Jan 2021is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa....
is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa. In hyperaccumulators, metal detoxification has also been linked or attributed to the activities of endophytes, and, in this regard, metal detoxification can be considered a form of endophytic behavior. Therefore, we report herein on the identification of proteins that confer heavy metal resistance, the in vitro characterization of heavy metal resistance, and the production of plant growth-promoting (PGP) volatiles by MAMP 4754. Multigenome comparative analyses of MAMP 4754 against eight other endophytic strains led to the identification of zinc, copper, and nickel resistance proteins in the genome of this endophyte. The maximum tolerance concentration (MTC) of this strain towards these metals was also investigated. The metal-exposed cells were analyzed by transmission electron microscopy (TEM). The ethyl acetate and chloroform extracts (1:1 /) of heavy metal untreated MAMP 4754 were also screened for the production of PGP compounds by Gas Chromatography-Mass Spectroscopy (GC/MS). The MTC was recorded at 15 mM, 4 mM, and 12 mM for zinc, copper, and nickel, respectively. The TEM analysis showed the accumulation of metals in the intracellular environment of MAMP 4754, while the GC/MS analysis revealed several plant growth-promoting compounds, including alcohols, phthalate esters, alkenes, ketones, sulfide derivatives, phenols, and thiazoles. Our findings suggest that the genetic makeup of MAMP 4754 encodes heavy metal resistant proteins that indicate hyperaccumulator-specific endophytic behavior and the potential for application in bioremediation. The production of plant growth-promoting volatiles in pure culture by MAMP 4754 is a characteristic feature for plant growth-promoting bacteria.
Topics: Combretum; Genomics; Metals, Heavy; Methylobacterium; Soil Pollutants; South Africa
PubMed: 33498657
DOI: 10.3390/ijerph18030997 -
MBio Jan 2021To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampled during 2 years at two Michigan sites and surveyed...
To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampled during 2 years at two Michigan sites and surveyed colonists by sequencing 16S rRNA gene amplicons. Mosaic and dynamic assemblages revealed the plant as a patchwork of tissue habitats that differentiated with age. Although assemblages primarily varied between roots and shoots, amplicon sequence variants (ASVs) also differentiated phyllosphere tissues. Increasing assemblage diversity indicated that variants dispersed more widely over time, decreasing the importance of stochastic variation in early colonization relative to tissue differences. As tissues underwent developmental transitions, the root and phyllosphere assemblages became more distinct. This pattern was driven by common variants rather than those restricted to a particular tissue or transiently present at one developmental stage. Patterns also depended critically on fine phylogenetic resolution: when ASVs were grouped at coarse taxonomic levels, their associations with host tissue and age weakened. Thus, the observed spatial and temporal variation in colonization depended upon bacterial traits that were not broadly shared at the family level. Some colonists were consistently more successful at entering specific tissues, as evidenced by their repeatable spatial prevalence distributions across sites and years. However, these variants did not overtake plant assemblages, which instead became more even over time. Together, these results suggested that the increasing effect of tissue type was related to colonization bottlenecks for specific ASVs rather than to their ability to dominate other colonists once established. Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed. In our study, phyllosphere tissues housed increasingly distinct microbial assemblages as plants aged, indicating that plants can be considered collections of tissue habitats in which microbial colonists-natural or synthetic-are established with differing success. Relationships between host genes and community diversity might vary depending on when samples are collected, given that assemblages grew more diverse as plants aged. Both spatial and temporal trends weakened when colonists were grouped by family, suggesting that functional rather than taxonomic profiling will be necessary to understand the basis for differences in colonization success.
Topics: Arabidopsis; Bacterial Typing Techniques; Flowers; Methylobacterium; Microbial Consortia; Oxalobacteraceae; Phylogeny; Plant Leaves; Plant Roots; Plant Shoots; RNA, Ribosomal, 16S
PubMed: 33468687
DOI: 10.1128/mBio.02723-20 -
Nucleic Acids Research Dec 2020Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture...
Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.
Topics: Amino Acid Sequence; Catalytic Domain; Cryptochromes; DNA Damage; DNA Repair; DNA, Single-Stranded; Deoxyribodipyrimidine Photo-Lyase; Methylobacterium; Pyrimidine Dimers; Rhodobacteraceae; Ultraviolet Rays
PubMed: 33270891
DOI: 10.1093/nar/gkaa1147 -
The Pan African Medical Journal 2020Appendicitis is one of the most common abdominal conditions requiring emergency surgery. However, acute appendicitis in patients with leukemia is a rare condition. We... (Review)
Review
Appendicitis is one of the most common abdominal conditions requiring emergency surgery. However, acute appendicitis in patients with leukemia is a rare condition. We report herein the case of an 18-year-old female with acute lymphoblastic leukemia (ALL), who was hospitalized in hematology department because of abdominal pain and fever. Ultrasound (US) of the abdomen revealed appendicitis and the patients underwent open appendectomy. The patient recovered without complications and was discharged in a good condition. The day of the operation blood and peritoneal fluid cultures were taken and Roseomonas gilardii was detected and healed empirically. The correct diagnosis of appendicitis in patients with leukemia and their management is challenging for physicians. Very rare microorganisms can be detected in these patients.
Topics: Acute Disease; Adolescent; Appendectomy; Appendicitis; Diagnosis, Differential; Female; Gram-Negative Bacterial Infections; Humans; Leukemia; Methylobacteriaceae
PubMed: 33117477
DOI: 10.11604/pamj.2020.36.283.24834 -
Biomolecules Oct 2020Cholecystokinin 1 receptor (CCK1R) is activated by singlet oxygen (O) generated in photodynamic action with sulphonated aluminum phthalocyanine (SALPC) or genetically...
Cholecystokinin 1 receptor (CCK1R) is activated by singlet oxygen (O) generated in photodynamic action with sulphonated aluminum phthalocyanine (SALPC) or genetically encoded protein photosensitizer (GEPP) KillerRed or mini singlet oxygen generator (miniSOG). A large number of GEPP with varied O quantum yields have appeared recently; therefore, in the present work, the efficacy of different GEPP to photodynamically activate CCK1R was examined, as monitored by Fura-2 calcium imaging. KillerRed, miniSOG, miniSOG2, singlet oxygen protein photosensitizer (SOPP), flavin-binding fluorescent protein from with point mutation C71G (Mr4511), and flavin-binding fluorescent protein from (DsFbFP) were expressed at the plasma membrane (PM) in AR4-2J cells, which express endogenous CCK1R. Light irradiation (KillerRed: white light 85.3 mW‧cm, 4' and all others: LED 450 nm, 85 mW·cm, 1.5') of GEPP-expressing AR4-2J was found to all trigger persistent calcium oscillations, a hallmark of permanent photodynamic CCK1R activation; DsFbFP was the least effective, due to poor expression. miniSOG was targeted to PM, mitochondria (MT) or lysosomes (LS) in AR4-2J in parallel experiments; LED light irradiation was found to all induce persistent calcium oscillations. In miniSOG-AR4-2J cells, light emitting diode (LED) light irradiation-induced calcium oscillations were readily inhibited by CCK1R antagonist devazepide 2 nM; miniSOG-AR4-2J cells were less susceptible, but miniSOG-AR4-2J cells were not inhibited. In conclusion, different GEPP could all photodynamically activate CCK1R. Intracellular GEPP photodynamic action may prove particularly suited to study intracellular GPCR.
Topics: Bacterial Proteins; Cell Line; Humans; Luminescent Proteins; Methylobacterium; Photosensitizing Agents; Receptors, Cholecystokinin; Recombinant Proteins; Rhodobacteraceae
PubMed: 33050050
DOI: 10.3390/biom10101423 -
Science Translational Medicine Sep 2020Dysbiosis of the skin microbiota is increasingly implicated as a contributor to the pathogenesis of atopic dermatitis (AD). We previously reported first-in-human safety... (Randomized Controlled Trial)
Randomized Controlled Trial
Dysbiosis of the skin microbiota is increasingly implicated as a contributor to the pathogenesis of atopic dermatitis (AD). We previously reported first-in-human safety and clinical activity results from topical application of the commensal skin bacterium for the treatment of AD in 10 adults and 5 children older than 9 years of age. Here, we examined the potential mechanism of action of treatment and its impact on children with AD less than 7 years of age, the most common age group for children with AD. In 15 children with AD, treatment was associated with amelioration of disease severity, improvement in epithelial barrier function, reduced burden on the skin, and a reduction in topical steroid requirements without severe adverse events. Our observed response rates to treatment were greater than those seen in historical placebo control groups in prior AD studies. Skin improvements and colonization by persisted for up to 8 months after cessation of treatment. Analyses of cellular scratch assays and the MC903 mouse model of AD suggested that production of sphingolipids by , cholinergic signaling, and flagellin expression may have contributed to therapeutic impact through induction of a TNFR2-mediated epithelial-to-mesenchymal transition. These results suggest that a randomized, placebo-controlled trial of treatment in individuals with AD is warranted and implicate commensals in the maintenance of the skin epithelial barrier.
Topics: Adult; Child; Dermatitis, Atopic; Eczema; Humans; Lipids; Methylobacteriaceae; Skin
PubMed: 32908007
DOI: 10.1126/scitranslmed.aaz8631 -
The New Phytologist Jan 2021Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined...
Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.
Topics: Bacteria; Microbiota; Plant Roots; Rhizosphere; Soil Microbiology
PubMed: 32852792
DOI: 10.1111/nph.16890