Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use ...2‐methylpropene (isobutene, 2‐MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2‐methylpropene derived from whole genome sequencing, differential expression analysis and peptide‐mass fingerprinting. Key genes identified are coding for a 4‐component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2‐hydroxyisobutyryl‐CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2‐methylpropene degraders.
Preterm premature rupture of membranes (PPROM), which is associated with vaginal dysbiosis, is responsible for up to one-third of all preterm births. Consecutive ascending colonization, infection, ...and inflammation may lead to relevant neonatal morbidity including early-onset neonatal sepsis (EONS). The present study aims to assess the vaginal microbial composition of PPROM patients and its development under standard antibiotic therapy and to evaluate the usefulness of the vaginal microbiota for the prediction of EONS. It moreover aims to decipher neonatal microbiota at birth as possible mirror of the in utero microbiota.
As part of the PEONS prospective multicenter cohort study, 78 women with PPROM and their 89 neonates were recruited. Maternal vaginal and neonatal pharyngeal, rectal, umbilical cord blood, and meconium microbiota were analyzed by 16S rRNA gene sequencing. Significant differences between the sample groups were evaluated using permutational multivariate analysis of variance and differently distributed taxa by the Mann-Whitney test. Potential biomarkers for the prediction of EONS were analyzed using the MetaboAnalyst platform.
Vaginal microbiota at admission after PPROM were dominated by Lactobacillus spp. Standard antibiotic treatment triggers significant changes in microbial community (relative depletion of Lactobacillus spp. and relative enrichment of Ureaplasma parvum) accompanied by an increase in bacterial diversity, evenness and richness. The neonatal microbiota showed a heterogeneous microbial composition where meconium samples were characterized by specific taxa enriched in this niche. The vaginal microbiota at birth was shown to have the potential to predict EONS with Escherichia/Shigella and Facklamia as risk taxa and Anaerococcus obesiensis and Campylobacter ureolyticus as protective taxa. EONS cases could also be predicted at a reasonable rate from neonatal meconium communities with the protective taxa Bifidobacterium longum, Agathobacter rectale, and S. epidermidis as features.
Vaginal and neonatal microbiota analysis by 16S rRNA gene sequencing after PPROM may form the basis of individualized risk assessment for consecutive EONS. Further studies on extended cohorts are necessary to evaluate how far this technique may in future close a diagnostic gap to optimize and personalize the clinical management of PPROM patients.
NCT03819192, ClinicalTrials.gov. Registered on January 28, 2019.
Agriculture and agribusiness generate waste rich in organic matter that can be degraded by biological processes and used as biomass for bioenergy. Inoculants to improve methane production in ...anaerobic reactors were developed using the anaerobic co-digestion of livestock manure (cattle, swine, and poultry) as biomass. These inoculants were prepared by anaerobic incubation of biomass with and without heating (constant at 35 °C and room temperature at 28 °C ± 3 °C, respectively) for 72 days. The identification of the microbiota in the inoculants, carried out by sequencing the amplicon of the 16S rRNA gene, showed differences between the inoculants in the two temperature conditions evaluated. Bacteroidetes was the most representative phylum in inoculants acclimated to ∼28 °C and Firmicutes in those inoculants acclimated to 35 °C. The inoculants were used as a starter of the anaerobic digestion process (livestock manure as biomass) in a 1 L anaerobic bioreactor for 77 days. The use of inoculants at room temperature (∼28 °C) improved the production of biogas and methane, reaching similar values to obtained at the ideal temperature (35 °C). The absence of heating probes in reactors conducted at room temperature resulted in a more favorable final energetic balance under this condition. The results are promising and show that it is possible to produce biogas in regions with temperatures slightly below those considered ideal for its production (35 °C) and highlight the economic viability of anaerobic digestion processes in such circumstances.
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•Inoculants acclimated at different temperatures present distinctive microbial structure.•Inoculants improve CH4 production in reactors at room temperature under daily variations.•Experiment conducted at room or constant ideal temperatures present similar CH4 production.•Reactors incubated at room temperature present higher energy gain than in constant 35 °C.•Biogas production at room temperature was feasible through the use of inoculants.
•First meiofauna description of the Atlantic Forest subtropical soil in South Brazil.•Pró-Mata soil seems to be at optimum ecological equilibrium.•Great diversity of species was found in Pró-Mata ...soil.
The assessment of environmental communities may lead to the identification of the novel or not-yet-classified organisms. Few studies have focused on the meiofauna of poorly known habitats such as native soils in subtropical forests. We surveyed eukaryotic communities inhabiting soil in an unexplored area of a native Atlantic Forest in southern Brazil using high-throughput sequencing. We analyzed a total of 281,400 sequences using V4 and V9 hypervariable regions of 18S rRNA gene. Opisthokonta was the most abundant supergroup, with Fungi and Metazoa representing an average of 40.6% and 15.8% of the sequences, respectively. Among the metazoan, Nematoda was the second most abundant phylum (4.8%). Isolation and morphological assessment 1745 specimens of nematodes, classified by functional feeding groups as plant parasites (35%), bacterial feeders (30%), omnivores (7%) and predators (5%). Specimens belonged to the class Chromadorea (89.6%) and Enoplea (10.4%).Approximately 65% of them could be morphologically classified only to order level. Results identified a considerable number of newly or still uncharacterized nematodes in soil biota in Atlantic Forest soils. Furthermore, this is the first study in this subtropical area to show that both high throughput sequencing and morphology can give complementary indications of the diversity of nematodes in soil samples.
Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a ...record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.
Live visualization of influenza A virus (IAV) structural proteins during viral infection in cells is highly sought objective to study different aspects of the viral replication cycle. To achieve ...this, we engineered an IAV to express a Tetra Cysteine tag (TC tag) from hemagglutinin (HA), which allows intracellular labeling of the engineered HA protein with biarsenic dyes and subsequent fluorescence detection. Using such constructs, we rescued a recombinant IAV with TC tag inserted in HA, in A/Puerto Rico/8/1934(H1N1) background (HA-TC). This recombinant HA-TC tag reporter IAV was replication-competent; however, as compared to wild type PR8 IAV, it was attenuated in multicycle replication. We confirmed expression of TC tag and biarsenical labeling of HA by immunofluorescence assay in cells infected with an HA-TC tag reporter IAV. Further, we used this reporter virus to visualize HA expression and translocation in IAV infected cells by live confocal imaging. We also tested the utility of the HA-TC IAV in testing chemical inhibitors of the HA translocation. Overall, HA-TC IAV is a versatile tool that will be useful for studying viral life cycle events, virus-host interactions, and anti-viral testing.
Presence of Archaea in dental caries biofilms Dame-Teixeira, Naile; de Cena, Jéssica Alves; Côrtes, Débora Azevedo ...
Archives of oral biology,
February 2020, 2020-Feb, 2020-02-00, 20200201, Letnik:
110
Journal Article
Recenzirano
•Archaeal sequences were detected in dental caries for the first time.•Archaeal diversity in the mouth is currently underestimated.•Archaeal diversity in caries does not seem to be a restriction on ...methanogens.•Primers direct to archaeal 16S rRNA could be better for archaeal taxonomy in dental caries.
Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.
To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.
The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.
Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.
Objective
The study aimed to investigate the pattern of oral yeast colonization of Sjögren's syndrome patients and its correlation to salivary flow rates, age, and time of the disease progression.
...Materials and methods
Saliva and swab specimens were obtained from 45 patients (primary Sjögren's syndrome = 15/ secondary Sjögren's syndrome = 15/ healthy controls = 15). Yeast species were identified using culture method through chromogenic medium followed by polymerase chain reaction and Sanger sequencing.
Results
Eleven species from six different genera were detected. The most prevalent species found was Candida albicans followed by Candida tropicalis, Candida glabrata, Candida parapsilosis, and Candida krusei. Both groups of Sjögren's syndrome showed higher counts of C. albicans (Total and CFU counts) when compared to control group. In contrast, a greater variety of yeast species was identified on samples of the control group.
Conclusions
This study showed that C. albicans is the most prevalent yeast, but also that a variety of other yeast species can colonize the oral cavity of Sjogren's syndrome patients. The identification of most of the colonies was not obtained by culturing‐PCR methods combined.
Papillon-Lefèvre syndrome (PLS) is an autosomal recessive rare disease, main characteristics of which include palmoplantar hyperkeratosis and premature edentulism due to advanced periodontitis ...(formerly aggressive periodontitis). This study aimed to characterize the oral phenotype, including salivary parameters, and the salivary microbiome of three PLS sisters, comparatively. Two sisters were toothless (PLSTL1 and PLSTL2), and one sister had most of the teeth in the oral cavity (PLST). Total DNA was extracted from the unstimulated saliva, and the amplicon sequencing of the 16S rRNA gene fragment was performed in an Ion PGM platform. The amplicon sequence variants (ASVs) were obtained using the DADA2 pipeline, and the taxonomy was assigned using the SILVA v.138. The main phenotypic characteristics of PLS were bone loss and premature loss of primary and permanent dentition. The PLST sister presented advanced periodontitis with gingival bleeding and suppuration, corresponding to the advanced periodontitis as a manifestation of systemic disease, stage IV, grade C. All three PLS sisters presented hyposalivation as a possible secondary outcome of the syndrome. Interestingly, PLST salivary microbiota was dominated by the uncultured bacteria
(F0058),
,
, and
(
domain).
,
, and
(
) dominated the microbiome of the PLSTL1 sister, while the PLSTL2 had higher abundances of
and
. This study was the first to show a high abundance of organisms belonging to the
domain comprising a core microbiome in human saliva. In conclusion, a PLST individual does have a microbiota different from that of the periodontitis' aggressiveness previously recognized. Due to an ineffective cathepsin C, the impairment of neutrophils probably provided a favorable environment for the PLS microbiome. The interactions of
F0058,
, and
with the microbial consortium of PLS deserves future investigation. Traditional periodontal therapy is not efficient in PLS patients. Unraveling the PLS microbiome is essential in searching for appropriate treatment and avoiding early tooth loss.
The aim of this study is to evaluate the effect of different thermal pretreatments of the inoculum on the diversity of the microbial community producing hydrogen from sugarcane vinasse. ...High-throughput sequencing of the 16S and 18S rRNA genes was performed. The reactor samples were also selected for the isolation of strict anaerobes. Decreased microbial diversity was observed with increasing pretreatment temperatures, with Firmicutes predominating: 90% to 97%. The highest abundance of
Staphylococcus
(7.9%) was found in pretreatment at 120 °C / 20 min at pH 6. The fungal analysis revealed a high prevalence of
Candida
(47%), Agaricomycetes, Pezizomycotina and
Aspergillus
in assays with higher H
2
production (90° C / 10 min at pH 6). Three species of Clostridium were isolated:
C. bifermentans
,
C. saccharoperbutylacetonicum
and
C. saccharobutylicum
. The isolates were tested separately and in co-cultures for the production of hydrogen. Hydrogen-producing capacity by co-culture of
Clostridium
species was increased by 18%. Knowing microorganisms and understanding the interaction between eukaryotes and prokaryotes is essential to obtain strategies for biotransformation of vinasse for the production of bioenergy.
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