Pseudomonas Tumuqiensis Sp. Nov., Isolated From Greenhouse Soil

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06T had the highest similarity with Pseudomonas cuatrocienegasensis 1NT was 97.4%. Phylogenetic analysis base on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that LAMW06T represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with the DNA G+C content of 63.5 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain LAMW06T and closely related members of Pseudomonas borbori R-20821T, Pseudomonas taeanensis MS-3T and Pseudomonas cuatrocienegasensis 1NT were 90.9%, 82.4%, 81.5 % and 43.0%, 25.9%, 24.6 % respectively. The major fatty acids contained summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C18:1 ω7c and C16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqiensis sp. nov. is proposed. The type strain is LAMW06T (=GDMCC 1.2003T =KCTC 72829T).

In Silico Study of the Effectiveness of 16S rRNA Gene as a Universal Genetic Marker to Identify Closely Related Burkholderia Spp. in Panicle Blight of Rice

The 16S rRNA gene is a housekeeping genetic marker that is available in almost all bacterial species and it is used in bacterial phylogeny and taxonomy studies. In many studies, the 16S rRNA gene is used in identification of certain bacterial species. Being a less conserved genetic marker, certain studies found it is a useful tool to infer the genome-wide similarity levels among the closely related prokaryotic organisms. Thus, this study aimed to compare the variation in the 16S rRNA partial region of Burkholderia spp. that infect the panicle of rice from eight different geographical areas. 58 sequences with total of 688 base pairs (bp) of 16S rRNA gene in B. glumae and B. gladioli were retrieved from public database based on several countries namely United State, Panama, Ecuador, Thailand, China, India, Korea and Malaysia. Then, the data sequences were analysed and validated using MEGAX and ABGD software respectively. The result of phylogenetic tree confirmed that B. glumae and B. gladioli were species that present in the panicle blight of rice. However, Data Analysis in Molecular Biology and Evolution (DAMBE) and Automatic Barcode Gap Discovery (ABGD) software were not able to detect substitution saturation and divergence between B. glumae and B. gladioli respectively based on the 58 sequences of the 16S rRNA partial region. Hence, it proves that 16S rRNA gene is an ineffective genetic marker to be used to differentiate the closely related species of bacteria from similar genus.

Hemotropic mycoplasmas in bats from forest fragments, state of Paraná, southern Brazil

The order Chiroptera is the second largest group of mammals with bats being identified as reservoir of several viral zoonoses, although, little is known about their role in other groups of pathogens, including hemotropic Mycoplasma spp. To date, hemoplasma species have been found infecting several species of bats with high genetic diversity between 16S rRNA gene sequences. On this study, we aimed to identify the occurrence and characterize 16S and 23S rRNA genes of hemoplasma species in four bats species (Artibeus lituratus, Carollia perspicillata, Sturnira lilium and Sturnira tildae) from forest fragments in Paraná State, southern Brazil, using PCR-based assays. Spleen tissue samples were collected, DNA extracted and further screened by a pan‑hemoplasma PCR assay. All samples consistently amplified the mammal endogenous gapdh gene. One out of 15 (6.66%; 95% CI: 0.2-31%) bats tested positive for hemotropic Mycoplasma sp. by the PCR assay targeting the 16S rRNA gene. Sequencing of the 16S rRNA gene fragment from the hemoplasma-positive bat showed 99.14% identity with hemotropic Mycoplasma sp. detected in Sturnira parvidens from Belize. Sequencing of the 23S rRNA gene fragment from the hemoplasma-positive bat showed 86.17% identity with ‘Candidatus Mycoplasma haemosphiggurus’ detected in orange-spined hairy dwarf porcupines (Sphiggurus villosus) from Southern Brazil.

Red Cusk-Eel (Genypterus chilensis) Gut Microbiota Description of Wild and Aquaculture Specimens

Chile has promoted the diversification of aquaculture and red cusk-eel (Genypterus chilensis) is one of the prioritized species. However, many aspects of the biology of the species are unknown or have little information available. These include intestinal microbiota, an element that may play an important role in the nutrition and defense of cultured animals for meat production. This study compares the microbiota composition of the intestinal contents of wild and aquaculture fish to explore the microbial communities present and their potential contribution to the host. DNA was extracted from the intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the Ion Torrent platform. After the examination of the sequences, strong differences were found in the composition at the level of phylum, being Firmicutes and Tenericutes the most abundant in aquaculture and wild condition, respectively. At the genus level, the Vagococcus (54%) and Mycoplasma (97%) were the most prevalent in the microbial community of aquaculture and wild condition, respectively. The evaluation of predicted metabolic pathways in these metagenomes showed that in wild condition there is an important presence of lipid metabolism belonging to the unsaturated fatty acid synthesis. In the aquaculture condition, the metabolism of terpenoids and polyketides were relevant. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of red cusk-eel (Genypterus chilensis) of wild and aquaculture origin using high-throughput sequencing.

Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing

Background Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota’s role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. Results Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. Conclusions This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.

Isolation of a Leuconostoc mesenteroides ssp. jonggajibkimchii strain from Parona leatherjacket (Parona signata): behavior in vegetal matrices fermentation

A Gram-positive, facultatively anaerobic, gas-forming, catalase-negative, nonmotile, non-sporeforming, vancomycin-resistant, and ovoid-shaped bacterium, designated strain Tw234, was isolated from the intestinal tract of Parona leatherjacket (Parona signata). The strain grew in the presence of 0–6% (w/v) NaCl, at pH 3.5–8.5 and 8–40 °C; optimum growth was achieved at 1% (w/v) NaCl, at pH 6.0 and 30–32 °C. Exopolysacharides production was detected by the solidification test of skim milk supplemented with sucrose in the temperature range of 8 to 30 °C. Results of phylogenetic analysis based on the 16S rRNA gene sequence similarity indicated that strain Tw234 was closed related to the genus Leuconostoc and 100% homology with the type strain Ln. mesenteroides ssp. jonggajibkimchii DRC1506 (KCCM 43249, JCM 31787). The evaluation of growth and acidification rates were carried out in white cabbage and Chinese cabbage and compared with the strain Ln. mesenteroides ssp. jonggajibkimchii RCTw1.1, isolated from the spontaneous fermentation of red cabbage. No significant differences were observed between the behaviors of the two strains. The strain Tw234 displayed higher growth and acidification rates in controlled fermentation of white cabbage compared with those obtained in Chinese cabbage. New trends are targeted on the isolation and selection of strains to achieve controlled fermentation of vegetables that may ensure uniform quality. The results obtained in this work suggest that strain Tw234 harbored technological useful properties for its potential use as a starter in controlled vegetable fermentations.

First Report of Potential Coral Disease in the Coral Hatchery of Thailand

In this study, coral disease was first reported in the coral hatchery in Thailand. Disease were usually found on corals aged two to five years old during the months of November to December of each year. To identify bacterial strains, culture-based methods for strain isolation and molecular techniques of the 16S rRNA gene analysis were used. The resuts showed that the dominant genera of bacteria in diseased corals were Vibrio spp. (comprising 41.01% of the isolates). The occurrence of the disease in the coral hatchery can have a significant effect on the health and survival of juvenile corals before being transplanted to natural reefs for restoration.

Description of Hydrogenophaga Crocea Sp. Nov. Associated With Cyanobacterial Mat Isolated From Farmland Mud

A catalase and oxidase-positive strain BA0156T was isolated from a cyanobacterial mat collected from the farmland mud cultivated with sugarcane from Ahmednagar, India. The 16S rRNA gene of strain BA0156T showed the highest percent sequence similarity with Hydrogenophaga borbori LMG 30805T (98.55 %), followed by H. flava DSM 619T (98.35 %) and H. intermedia DSM 5680T (98.21 %). The strain BA0156T consisted of major fatty acids, C16:0 (25.1 %) and C17:0 cyclo (3.9 %), whereas phosphatidylethanolamine and diphosphatidylglycerol were the major polar lipids. The OrthoANI and dDDH values between strain BA0156T and its closest relative H. borbori LMG 30805T were 84.59 % and 28.3 %, respectively. The DNA G+C content of strain BA0156T was 69.42 mol %. Furthermore, the biochemical and physiological features of strain BA0156T showed a distinct pattern from their closest phylogenetic neighbours. The phenotypic, genotypic and chemotaxonomic characteristics indicated that the strain BA0156T represents a new species for which the name Hydrogenophaga crocea (type strain BA0156 T = MCC 3062T = KCTC 72452T = JCM 34507T) is proposed.

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

An actinobacterial strain designated MMS20-R1-14T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10–40 °C (optimum, 37 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002T (99.51 %) and Micromonospora rifamycinica AM105T (99.37 %). The orthoANI values between strain MMS20-R1-14T and the two type strains were 95.72 and 90.99 %, and the digital DNA–DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14T from its mostly related species. The DNA G+C content of strain MMS20-R1-14T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C18 : 1 ω9c, iso-C15 : 0 and iso-C16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H4) and MK-10(H6), all of which were consistent with those of Micromonospora . Strain MMS20-R1-14T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14T merits recognition as representing a novel species of the genus Micromonospora , for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14T=KCTC 49541T=JCM 34494T) is proposed.

Rheinheimera lutimaris sp. nov., a marine bacterium isolated from coastal sediment

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-2T, was isolated from coastal sediment sampled in Jiangsu Province and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 28 °C (range 4–38 °C) and pH 7 (pH 6–10). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YQF-2T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera pacifica KMM 1406T (98.6%), followed by Rheinheimera aestuarii H29T (98.4%), Rheinheimera japonica KMM 9513T (98.3%), Rheinheimera aquimaris SW-353T (98.3%), Rheinheimera hassiensis E48T (97.8%) and Rheinheimera muenzenbergensis E49T (97.7%). The 16S rRNA gene sequence identities between strain YQF-2T and other members of the genus Rheinheimera were below 97.2%. The digital DNA–DNA hybridization value between strain YQF-2T and R. pacifica KMM 1406T was 23.3±2.3%. The average nucleotide identity value between strain YQF-2T and R. pacifica KMM 1406T was 79.7%. The unique respiratory quinone was ubiquinone-8. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The strain had summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C12:0 3-OH and iso-C17:0 3-OH as major fatty acids. The G+C content of the genomic DNA was 50.0 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-2T represents a novel species of the genus Rheinheimera , for which the name Rheinheimera lutimaris sp. nov. is proposed, with the type strain YQF-2T (=KCTC 72184T=MCCC 1K03663T).