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International Journal of Systematic and... Nov 2021Two novel bacterial strains, designated as DN00404 and DN04309, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of...
Two novel bacterial strains, designated as DN00404 and DN04309, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404 and DN04309 were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404 were short rod-shaped and those of DN04309 were long rod-shaped. Strain DN00404 was found to grow at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.5) and in 0-2.0 % (w/v) NaCl (optimum, 1.0 %). Strain DN04309 was found to grow at 15-45 °C (optimum, 20-37 °C), at pH 5.5-11.0 (optimum, 7.5) and in 0-4.0 % (w/v) NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0-96.0 % ANI and 70.0 % dDDH for species delineation. The genomic DNA G+C contents of strains DN00404 and DN04309 were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C and summed feature 3 (C 6 and/or C 7), which were similar to those of other species of this genus. The two major fatty acids C and iso-C 3-OH were also found in strain DN00404. Based on genotypic and phenotypic characteristics, two novel species of the genus are proposed: sp. nov. with DN00404 (=GDMCC 1.1865=KACC 21924) as the type strain and sp. nov. with DN04309 (=GDMCC 1.1984=KCTC 82348) as the type strain.
Topics: Aquaculture; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium; Water
PubMed: 34779757
DOI: 10.1099/ijsem.0.005091 -
Microorganisms Mar 2023Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet...
Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet little is known about the impact of their microbiomes on tadpole health. This study provides a first characterization of the microbiome of foam nests from three species of Leptodactylids (, , and ) by investigating the DNA extracted from foam nests, adult tissues, soil, and water samples, analyzed via 16S rRNA gene amplicon sequencing to gain insight into the factors driving its composition. The results showed that the dominant phyla were proteobacteria, bacteroidetes, and firmicutes, with the most abundant genera being , , and . The foam nest microbiomes of and were more similar to each other than to that of , despite their phylogenetic distance. The foam nests demonstrated a distinct microbiome that clustered together and separated from the microbiomes of the environment and adult tissue samples. This suggests that the peculiar foam nest composition shapes its microbiome, rather than vertical or horizontal transference forces. We expanded this knowledge into amphibian foam nest microbiomes, highlighting the importance of preserving healthy foam nests for amphibian conservation.
PubMed: 37110323
DOI: 10.3390/microorganisms11040900 -
Applied and Environmental Microbiology Dec 2022Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and...
Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, , , and were characteristic for 3-month-old litter, and , , , and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.
Topics: Animals; Chickens; RNA, Ribosomal, 16S; Microbiota; Cecum
PubMed: 36468876
DOI: 10.1128/aem.01809-22 -
Microbiome Mar 2022The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure...
BACKGROUND
The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood.
METHODS
Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.
RESULTS
Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.
CONCLUSIONS
Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.
Topics: Animals; Anura; Chytridiomycota; Microbiota; Mycoses; RNA, Ribosomal, 16S
PubMed: 35272699
DOI: 10.1186/s40168-021-01215-6 -
Bioresource Technology Apr 2022Imidacloprid (CHClNO) is the most widely used insecticide. Its persistence and toxic nature have caused a detrimental effect on living biota. Thus its removal from the...
Imidacloprid (CHClNO) is the most widely used insecticide. Its persistence and toxic nature have caused a detrimental effect on living biota. Thus its removal from the contaminated environment has become imperative. The present study aimed to isolate bacterial species from pesticide-contaminated sites and assess their potential for biodegradation of imidacloprid. The 16S rRNA analysis revealed the genetic relatedness of isolates to Sphingobacterium sp., Agrobacterium sp., Pseudomonas sp., and Bacillus sp. Batch biodegradation studies showed that Sphingobacterium sp. and Agrobacterium sp. were the most promising isolates as they degraded 81.0% and 84.9%, respectively, of imidacloprid at the concentration of 95 mg/L via co-metabolism. Kinetic study (V/K ratio) also suggested the high degradation efficiency of these isolates. Imidacloprid-guanidine (CHClN) was identified as the metabolite. This report highlights the potential of bacteria for imidacloprid degradation and could be utilized for the formulation of strategies for the remediation of imidacloprid contaminated environments.
Topics: Biodegradation, Environmental; Kinetics; Neonicotinoids; Nitro Compounds; RNA, Ribosomal, 16S
PubMed: 35231595
DOI: 10.1016/j.biortech.2022.126915 -
International Journal of Systematic and... Jan 2022An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel...
An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1 was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria-Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C, summed feature 3 (C 6 and/or C 7) and iso-C 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1 was affiliated with the genus and had the highest sequence similarity to h337 (97.0 %) and HER1398 (95.6 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain C459-1 and h337 were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1 from other species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1 represents a novel species of the genus , for which the name sp. nov. is proposed, with strain is C459-1 (CGMCC 1.18716=KCTC 82381) as the type strain.
Topics: Animals; Bacterial Typing Techniques; Base Composition; Camelus; Carbon-Carbon Lyases; DNA, Bacterial; Fatty Acids; Feces; Glycolipids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium
PubMed: 35100101
DOI: 10.1099/ijsem.0.005215 -
Frontiers in Medicine 2022Most colorectal cancer (CRC) cases are sporadic and develop along the adenoma-carcinoma sequence. Intestinal microbial dysbiosis is involved in the development of...
BACKGROUND
Most colorectal cancer (CRC) cases are sporadic and develop along the adenoma-carcinoma sequence. Intestinal microbial dysbiosis is involved in the development of colorectal cancer. However, there are still no absolute markers predicting the progression from adenoma to carcinoma. This study aimed to investigate the characteristics of intestinal microbiota in patients with colorectal adenoma and carcinoma and its correlations with clinical characteristics.
METHODS
Fecal samples were collected from 154 patients with CRC, 20 patients with colorectal adenoma (AD) and 199 healthy controls. To analyze the differences in the intestinal microbiota, 16S rRNA gene sequencing was conducted.
RESULTS
At the genus level, there were four significantly different genera among the three groups, namely Acidaminococcus, Alloprevotella, Mycoplasma, and Sphingobacterium, while Acidaminococcus significantly decreased with the order of Control-AD-CRC ( < 0.05). In addition, Parvimonas, Peptostreptococcus, Prevotella, Butyricimonas, Alistipes, and Odoribacter were the key genera in the network of colorectal adenoma/carcinoma-associated bacteria. The top 10 most important species, including , , , , , , , , and , showed the best performance in distinguishing AD from CRC (AUC = 85.54%, 95% CI: 78.83-92.25%). The clinicopathologic features, including age, gender, tumor location, differentiation degree, and TNM stage, were identified to be closely linked to the intestinal microbiome in CRC.
CONCLUSION
Several intestinal bacteria changed along the adenoma-carcinoma sequence and might be the potential markers for the diagnosis and treatment of colorectal adenoma/carcinoma. Intestinal microbiota characteristics in CRC should account for the host factors.
PubMed: 35935780
DOI: 10.3389/fmed.2022.888340 -
International Journal of Systematic and... Nov 2020Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7 and 30C10-4-7, were isolated from bark canker tissue of , respectively. 16S rRNA gene sequence...
Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7 and 30C10-4-7, were isolated from bark canker tissue of , respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7 shows 98.0 % sequence similarity to DSM 7418, and strain 30C10-4-7 shows highest sequence similarity to H-12 (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7 is a novel member different from recognized species in the genus . The main fatty acids and respiratory quinone detected in strain 36D10-4-7 are C 7 and/or C 6 and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7, the major fatty acids and menaquinone are iso-C, C 7 and/or C 6 and iso-C 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera and . The name sp. nov. (type strain 36D10-4-7=CFCC 13112=KCTC 52799) and sp. nov. (type strain 30C10-4-7=CFCC 13069=KCTC 52797) are proposed.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Plant Bark; Plant Diseases; Populus; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium; Sphingomonas; Ubiquinone
PubMed: 32924914
DOI: 10.1099/ijsem.0.004451 -
Organoarsenical tolerance in Sphingobacterium wenxiniae, a bacterium isolated from activated sludge.Environmental Microbiology Feb 2022Organoarsenicals enter the environment from biogenic and anthropogenic sources. Trivalent inorganic arsenite (As(III)) is microbially methylated to more toxic...
Organoarsenicals enter the environment from biogenic and anthropogenic sources. Trivalent inorganic arsenite (As(III)) is microbially methylated to more toxic methylarsenite (MAs(III)) and dimethylarsenite (DMAs(III)) that oxidize in air to MAs(V) and DMAs(V). Sources include the herbicide monosodium methylarsenate (MSMA or MAs(V)), which is microbially reduced to MAs(III), and the aromatic arsenical roxarsone (3-nitro-4-hydroxybenzenearsonic acid or Rox), an antimicrobial growth promoter for poultry and swine. Here we show that Sphingobacterium wenxiniae LQY-18 , isolated from activated sludge, is resistant to trivalent MAs(III) and Rox(III). Sphingobacterium wenxiniae detoxifies MAs(III) and Rox(III) by oxidation to MAs(V) and Rox(V). Sphingobacterium wenxiniae has a novel chromosomal gene, termed arsU1. Expressed in Escherichia coli arsU1 confers resistance to MAs(III) and Rox(III) but not As(III) or pentavalent organoarsenicals. Purified ArsU1 catalyses oxidation of trivalent methylarsenite and roxarsone. ArsU1 has six conserved cysteine residues. The DNA sequence for the three C-terminal cysteines was deleted, and the other three were mutated to serines. Only C45S and C122S lost activity, suggesting that Cys45 and Cys122 play a role in ArsU1 function. ArsU1 requires neither FMN nor FAD for activity. These results demonstrate that ArsU1 is a novel MAs(III) oxidase that contributes to S. wenxiniae tolerance to organoarsenicals.
Topics: Animals; Arsenic; Arsenicals; Roxarsone; Sewage; Sphingobacterium; Swine
PubMed: 33998126
DOI: 10.1111/1462-2920.15599 -
International Journal of Systematic and... Feb 2018A novel Gram-negative, rod shaped, non-motile bacterium, designated strain YK2, was isolated from yak milk from Leh, India. The strain was positive for oxidase- and...
A novel Gram-negative, rod shaped, non-motile bacterium, designated strain YK2, was isolated from yak milk from Leh, India. The strain was positive for oxidase- and catalase-activities and negative for starch hydrolysis, nitrate reduction, citrate utilization, urease, lysine decarboxylase and ornithine decarboxylase activities. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH (summed feature 3). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and six unidentified lipids. The DNA G+C content of the strain was 38.9 mol%. The 16S rRNA gene sequence analysis indicated that strain YK2 was a member of the genus Sphingobacterium and closely related to Sphingobacterium alimentarium and Sphingobacterium composti with pair-wise sequence similarity of 98.3 and 97.9 %, respectively. The sequence similarity to other members of the genus Sphingobacterium was between 92.6 to 96.3 %. Phylogenetic analysis showed that strain YK2 clustered with Sphingobacterium alimentarium and together clustered with Sphingobacterium composti. DNA-DNA hybridization of strain YK2 with Sphingobacterium alimentarium WCC 4521 and Sphingobacterium composti T5-12 showed a relatedness of only 38 and 54 %, respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain YK2 represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium bovisgrunnientis sp. nov. is proposed. The type strain of Sphingobacterium bovisgrunnientis sp. nov. is YK2 (=MTCC 12631=KCTC 52685=JCM 31951).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Cattle; DNA, Bacterial; Fatty Acids; India; Milk; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium
PubMed: 29388539
DOI: 10.1099/ijsem.0.002562