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Fulltext Metabolic potential of the moderate halophile Yangia sp. ND199 for co-production of polyhydroxyalkanoates and exopolysaccharides

Romero Soto L, Thabet H, Maghembe R, Gameiro D, Van-Thuoc D, Dishisha T, et al.

Microbiologyopen, 2021 01;10(1):e1160.
PMID: 33650793 DOI: 10.1002/mbo3.1160

Yangia sp. ND199 is a moderately halophilic bacterium isolated from mangrove samples in Northern Vietnam, which was earlier reported to grow on several sugars and glycerol to accumulate poly(hydroxyalkanoates) (PHA). In this study, the potential of the bacterium for co-production of exopolysaccharides (EPS) and PHA was investigated. Genome sequence analysis of the closely related Yangia sp. CCB-M3 isolated from mangroves in Malaysia revealed genes encoding enzymes participating in different EPS biosynthetic pathways. The effects of various cultivation parameters on the production of EPS and PHA were studied. The highest level of EPS (288 mg/L) was achieved using sucrose and yeast extract with 5% NaCl and 120 mM phosphate salts but with modest PHA accumulation (32% of cell dry weight, 1.3 g/L). Growth on fructose yielded the highest PHA concentration (85% of CDW, 3.3 g/L) at 90 mM phosphate and higher molecular weight EPS at 251 mg/L yield at 120 mM phosphate concentration. Analysis of EPS showed a predominance of glucose, followed by fructose and galactose, and minor amounts of acidic sugars.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Geography as non-genetic modulation factor of chicken cecal microbiota

Pin Viso N, Redondo E, Díaz Carrasco JM, Redondo L, Sabio Y Garcia J, Fernández Miyakawa M, et al.

PLoS One, 2021;16(1):e0244724.
PMID: 33406150 DOI: 10.1371/journal.pone.0244724

The gastrointestinal tract of chickens harbors a highly diverse microbiota contributing not only to nutrition, but also to the physiological development of the gastrointestinal tract. Microbiota composition depends on many factors such as the portion of the intestine as well as the diet, age, genotype, or geographical origin of birds. The aim of the present study was to demonstrate the influence of the geographical location over the cecal microbiota from broilers. We used metabarcoding sequencing datasets of the 16S rRNA gene publicly available to compare the composition of the Argentine microbiota against the microbiota of broilers from another seven countries (Germany, Australia, Croatia, Slovenia, United States of America, Hungary, and Malaysia). Geographical location played a dominant role in shaping chicken gut microbiota (Adonis R2 = 0.6325, P = 0.001; Mantel statistic r = 0.1524, P = 4e-04) over any other evaluated factor. The geographical origin particularly affected the relative abundance of the families Bacteroidaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. Because of the evident divergence of microbiota among countries we coined the term "local microbiota" as convergent feature that conflates non-genetic factors, in the perspective of human-environmental geography. Local microbiota should be taken into consideration as a native overall threshold value for further appraisals when testing the production performance and performing correlation analysis of gut microbiota modulation against different kind of diet and/or management approaches. In this regard, we described the Argentine poultry cecal microbiota by means of samples both from experimental trials and commercial farms. Likewise, we were able to identify a core microbiota composed of 65 operational taxonomic units assigned to seven phyla and 38 families, with the four most abundant taxa belonging to Bacteroides genus, Rikenellaceae family, Clostridiales order, and Ruminococcaceae family.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext PHYLOGENETIC ANALYSIS OF Komagataeibacter sp.: A CELLULOSE-PRODUCER BACTERIA BASED ON 16S rRNA GENE SEQUENCES+-

Nur Aisyah Atikah Alizan, Sarah S. Zakaria

Journal of Academia Universiti Teknologi MARA Negeri Sembilan, 2021;9(1):97-105.
MyJurnal

Bacteria of the genus Komagataeibacter are described to be the most noteworthy for having several of its species being efficient and strong cellulose producers. The 16S ribosomal RNA (rRNA) gene analysis is often used for the identification and taxonomic classification of these bacteria species. In order to observe the phylogenetic relationship among Komagataeibacter sp., twelve sequences of the 16S rRNA gene with three sequences each for species namely Komagataeibacter europaeus, Komagataeibacter hansenii, Komagataeibacter intermedius and Komagataeibacter xylinus were retrieved from NCBI GenBank database. The sequences were aligned and analysed using PAUP, OrthoANI and BLAST, followed by the phylogenetic tree construction using a Maximum Likelihood method. The parsimony character diagnostic analysis showed very few numbers of parsimony- informative characters present in the aligned sequences which is only 1.5% of the total characters. The inferred phylogenetic relationships demonstrated the unexpected positioning of K. xylinus (GQ240638: Gluconacetobacter xylinus strain) and K. xylinus (KC11853: G. xylinus strain) into the clades of K. europaeus and K. hansenii respectively. The also very low bootstrap values of the branch points linking the K. europaeus species indicated low support for the produced topologies. The findings of this study indicate that more phylogenies information can be attained by increasing the taxon sampling. In addition, more robust molecular data are needed to infer the phylogenetic relationships between the Komagataeibacter species more accurately.

Matched MeSH terms: RNA, Ribosomal, 16S
Increasing Reproducibility in Oral Microbiome Research

Gopinath D, Menon RK

Methods Mol Biol, 2021;2327:1-15.
PMID: 34410636 DOI: 10.1007/978-1-0716-1518-8_1

Evidence on the role of the oral microbiome in health and disease is changing the way we understand, diagnose, and treat ailments. Numerous studies on diseases affecting the oral cavity have revealed a large amount of data that is invaluable for the advancements in diagnosing and treating these diseases. However, the clinical translation of most of these exploratory data is stalled by variable methodology between studies and non-uniform reporting of the data.Understanding the key areas that are gateways to bias in microbiome studies is imperative to overcome this challenge faced by oral microbiome research. Bias can be multifactorial and may be introduced in a microbiome research study during the formulation of the study design, sample collection and storage, or the sample processing protocols before sequencing. This chapter summarizes the recommendations from literature to eliminate bias in the microbiome research studies and to ensure the reproducibility of the microbiome research data.

Matched MeSH terms: RNA, Ribosomal, 16S
Bacterial endosymbiont inhabiting Leucaena leucocephala leaves and their antioxidant and antidiabetic potential

Chigurupati S, Vijayabalan S, Selvarajan KK, Alhowail A, Kauser F

J Complement Integr Med, 2020 Dec 22;18(2):319-325.
PMID: 34187119 DOI: 10.1515/jcim-2020-0203

OBJECTIVES: Research on endosymbionts is emerging globally and is considered as a potential source of bioactive phytochemicals. The present study examines the antioxidant and antidiabetic of the endophytic crude extract isolated from Leucaena leucocephala leaves.
METHODS: Endophytic bacteria were isolated from the leaves of L. leucocephala and 16S rRNA gene sequencing was used to establish their identity. The in vitro antioxidant effect of endophytic crude extract (LL) was evaluated using 2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) free radical scavenging methods. The in vitro antidiabetic properties of LL were evaluated using α-amylase and α-glucosidase enzyme inhibition assay.
RESULTS: The isolated endophytic bacteria were identified as Cronobacter sakazakii. LL displayed potent free radical scavenging effect against ABTS and DPPH radicals with an inhibitory concentration 50% (IC50) value of 17.49 ± 0.06 and 11.3 ± 0.1 μg/mL respectively. LL exhibited α-amylase and α-glucosidase inhibition with an IC50 value of 23.3 ± 0.08 and 23.4 ± 0.1 μg/mL respectively compared to the standard drug (acarbose). Both glucose loaded normoglycemic rats and STZ induced diabetic rats treated with LL (200 mg/kg) exhibited a considerable reduction in blood glucose levels p<0.01 after 8 h of treatment when compared to normal and diabetic control rats respectively.
CONCLUSIONS: Thus, the study shows that LL has a wellspring of natural source of antioxidants, and antidiabetic agents and phytoconstituents present in endophytes could be the rich source for bioactive compounds.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Rapid shifts in methanotrophic bacterial communities mitigate methane emissions from a tropical hydropower reservoir and its downstream river

Reis PCJ, Ruiz-González C, Crevecoeur S, Soued C, Prairie YT

Sci Total Environ, 2020 Dec 15;748:141374.
PMID: 32823225 DOI: 10.1016/j.scitotenv.2020.141374

Methane-oxidizing bacteria (MOB) present in the water column mitigate methane (CH4) emissions from hydropower complexes to the atmosphere. By creating a discontinuity in rivers, dams cause large environmental variations, including in CH4 and oxygen concentrations, between upstream, reservoir, and downstream segments. Although highest freshwater methanotrophic activity is often detected at low oxygen concentrations, CH4 oxidation in well-oxygenated downstream rivers below dams has also been reported. Here we combined DNA and RNA high-throughput sequencing with microscopic enumeration (by CARD-FISH) and biogeochemical data to investigate the abundance, composition, and potential activity of MOB taxa from upstream to downstream waters in the tropical hydropower complex Batang Ai (Malaysia). High relative abundance of MOB (up to 61% in 16S rRNA sequences and 19% in cell counts) and enrichment of stable isotopic signatures of CH4 (up to 0‰) were detected in the hypoxic hypolimnion of the reservoir and in the outflowing downstream river. MOB community shifts along the river-reservoir system reflected environmental sorting of taxa and an interrupted hydrologic connectivity in which downstream MOB communities resembled reservoir's hypolimnetic communities but differed from upstream and surface reservoir communities. In downstream waters, CH4 oxidation was accompanied by fast cell growth of particular MOB taxa. Our results suggest that rapid shifts in active MOB communities allow the mitigation of CH4 emissions from different zones of hydropower complexes, including in quickly re-oxygenated rivers downstream of dams.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation

Hamood Altowayti WA, Almoalemi H, Shahir S, Othman N

Ecotoxicol Environ Saf, 2020 Dec 01;205:111267.
PMID: 32992213 DOI: 10.1016/j.ecoenv.2020.111267

Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Metagenomic data of bacterial community from different land uses at the river basin, Kelantan

Rupert R, Lie GJCW, John DV, Annammala KV, Jani J, Rodrigues KF

Data Brief, 2020 Dec;33:106351.
PMID: 33072827 DOI: 10.1016/j.dib.2020.106351

The data provided in the article includes the sequence of bacterial 16S rRNA gene from a high conservation value forest, logged forest, rubber plantation and oil palm plantation collected at Kelantan river basin. The logged forest area was previously notified as a flooding region. The total gDNA of bacterial community was amplified via polymerase chain reaction at V3-V4 regions using a pair of specific universal primer. Amplicons were sequenced on Illumina HiSeq paired-end platform to generate 250 bp paired-end raw reads. Several bioinformatics tools such as FLASH, QIIME and UPARSE were used to process the reads generated for OTU analysis. Meanwhile, R&D software was used to construct the taxonomy tree for all samples. Raw data files are available at the Sequence Read Archive (SRA), NCBI and data information can be found at the BioProject and BioSample, NCBI. The data shows the comparison of bacterial community between the natural forest and different land uses.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Whole genome sequencing data of a clinical Enterococcus gallinarum strain EGR748 from Sabah, Malaysia

Mastor NN, Subbiah VK, Bakar WNWA, Begum K, Alam MJ, Hoque MZ

Data Brief, 2020 Dec;33:106370.
PMID: 33102652 DOI: 10.1016/j.dib.2020.106370

Enterococcus gallinarum is a gram positive facultatively anaerobic bacteria that is typically found in mammalian intestinal tracts. It is generally not considered pathogenic to humans and is rarely reported. Here, we present the draft genome sequence data of Enterococcus gallinarum strain EGR748 isolated from a human clinical sample, and sequenced using the Illumina HiSeq 4000 system. The estimated whole genome size of the strain was 3,730,000 bp with a G + C content of 40.43%. The de novo assembly of the genome generated 55 contigs with an N50 of 208,509 bp. In addition, the Maximum Likelihood phylogenetic analysis based on the 16S rRNA sequence data accurately clustered EGR748 with other E. gallinarum strains. The data may be useful to demonstrate the capacity of this enterococcal species becoming the causal agents of nosocomial blood-stream infections. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAABOR000000000.

Matched MeSH terms: RNA, Ribosomal, 16S
Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest

Goh CBS, Wong LW, Parimannan S, Rajandas H, Loke S, Croft L, et al.

Int J Syst Evol Microbiol, 2020 Dec;70(12):6355-6363.
PMID: 33146596 DOI: 10.1099/ijsem.0.004539

A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39' 04.7' N 101° 17' 43.7'' E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA-DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Exploring the potential of halotolerant bacteria for biodegradation of polycyclic aromatic hydrocarbon

Al Farraj DA, Hadibarata T, Yuniarto A, Alkufeidy RM, Alshammari MK, Syafiuddin A

Bioprocess Biosyst Eng, 2020 Dec;43(12):2305-2314.
PMID: 32812060 DOI: 10.1007/s00449-020-02415-4

The present study aimed to determine the degradation and transformation of three-ring PAHs phenanthrene and anthracene by Cryptococcus sp. MR22 and Halomonas sp. BR04 under halophilic conditions. The growth progress of Cryptococcus sp. MR22 and Halomonas sp. BR04 on anthracene and phenanthrene was monitored by colony-forming unit (CFU) technique. The growth of the bacteria was maintained at a maximum concentration of 200 mg/L of all tested hydrocarbon, indicating that Cryptococcus sp. MR22 and Halomonas sp. BR04 significantly perform in the removal of the PAH-contaminated medium at low concentrations. The fit model to represent the biodegradation kinetics of both PAHs was first-order rate equation The extract prepared from cells supplemented with three different substrates exhibited some enzymes such as hydroxylase, dioxygenase, laccase and peroxidase. The results suggest that both strains had an impressive ability in the degradation of aromatic and aliphatic hydrocarbon but also could tolerate in the extreme salinity condition.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

Choo SW, Rishik S, Wee WY

Microb Genom, 2020 12;6(12).
PMID: 33295861 DOI: 10.1099/mgen.0.000495

Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Subspecies 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina

Chua KO, See-Too WS, Tan JY, Song SL, Yong HS, Yin WF, et al.

J Microbiol, 2020 Dec;58(12):988-997.
PMID: 33095388 DOI: 10.1007/s12275-020-0325-8

In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15-37°C (optimum, 28-30°C) and in the presence of 0-1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1ω7c, C16:0, C19:0ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56-94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteaceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Detection of Bartonella sp. in ticks and their small mammal hosts in mangrove forests of Peninsular Malaysia

Asyikha R, Sulaiman N, Mohd-Taib FS

Trop Biomed, 2020 Dec 01;37(4):919-931.
PMID: 33612746 DOI: 10.47665/tb.37.4.919

Bacteria of the genus Bartonella have been known as emerging zoonotic pathogens for several human diseases including cat scratch disease, Carrion's disease and trench fever. Numerous species of small mammals have been reported to play a role as a suitable reservoir to many pathogenic Bartonella. These infections are thought to be transmitted through blood-feeding arthropod vectors such as ticks, fleas and lice. The purpose of this study is to detect the presence of Bartonella species from tick samples collected from small mammals in mangrove forests of Peninsular Malaysia. Herein, 38 individual ticks and their small mammals host were evaluated for the presence of Bartonella DNA by conventional PCR targeting the 16S rRNA intergenic spacer region (ITS) and partial sequencing of 460 bp from this locususing Bartonella genus-specific primers. Two tick individuals from Dermacentor auratus and Haemaphysalis hystricis collected from Rattus tiomanicus (host), were PCR-positive for Bartonella DNA amplification. No Bartonella amplification was possible in other tick species (Amblyomma sp.). Phylogenetic analysis of ITS fragments demonstrated that the sequences from ticks were closely related to Bartonella phoceensis, a species that has been reported from black rats (Rattus rattus) in Australia. This is the first report of a Bartonella bacteria detected in ticks from small mammals in Malaysia. Further research should be warranted to investigate the transmission of Bartonella and the potential impact of this zoonotic pathogen in animals and humans as this mangrove ecosystem is significant for local economy and tourism.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Bacterial profiling of head lice isolated from the Orang Asli: A first report in Malaysia

Abd Majid MA, Khoo JJ, Lim FS, Khor CS, Loong SK, Low VL, et al.

Trop Biomed, 2020 Dec 01;37(4):884-895.
PMID: 33612742 DOI: 10.47665/tb.37.4.884

This study was carried out to determine from bacterial profiling to the bacterial profiles of head lice among the Orang Asli communities. The head lice were collected from Orang Asli community volunteers. The surface sterilized head lice pools were subjected to genomic DNA extraction while next generation sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform. Six female and three male head lice identified as Pediculus humanus capitis were collected. A total of 111 368 number of NGS sequencing reads were recorded while another 223 bacterial taxa sequences were obtained. Symbiotic bacteria showed the highest number of reads, with Arsenophonus and Rhodococcus sequences being the most abundant genera in the female and male samples, respectively. The female head lice contained a more distinct microbial diversity. Amongst the pathogenic bacterial species sequences noted were the methicillin-resistant Staphylococcus aureus, Streptobacillus moniliformis, Haemophilus influenzae, Bordetella pertussis and Acinetobacter baumannii. The 16S rRNA genome sequencing revealed a number of rare and pathogenic bacterial species within the head lice of the Orang Asli. The socio-economic practices of the community which involved forest foraging and hunting, and their poor living conditions potentially facilitated the transmission of zoonotic bacterial pathogens, including those found within the head lice. Hence, there is the possibility that the head lice could serve as vectors for the transmission of pathogenic bacteria. This study highlighted the diverse microbial community found within the head lice's gut of the Orang Asli, with the detection of multiple rare and pathogenic bacteria capable of causing severe infections.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext The complete mitochondrial genome of Amyda cartilaginea (Testudines: Trionychidae)

Cui L, Rao D, Zhang M

Mitochondrial DNA B Resour, 2020 Nov 03;5(3):3670-3672.
PMID: 33367054 DOI: 10.1080/23802359.2020.1832595

The Asiatic softshell turtle, also known as the black-rayed softshell turtle (Amyda cartilaginea; Accession no: MT039230), is found in northeastern India (Mizoram), Brunei Darussalam, Indonesia, Malaysia, Singapore, Myanmar, Laos, Vietnam, Cambodia, and Thailand. This turtle is thought to have been introduced into the Sunda Islands, Sulawesi, and Yunnan, China, through the Malay Peninsula to Sumatra, Java, and Borneo. Herein, we determined the complete mitochondrial genome of A. cartilaginea for the first time using next-generation sequencing (NGS). The assembled mitogenome was 16,763 bp in length and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (CR). The PCGs based maximum-likelihood phylogeny discriminated A. cartilaginea from other Testudines and clusters within family Trionychidae with the sister taxa of Nilssonia nigricans.

Matched MeSH terms: RNA, Ribosomal, 16S
An efficient oxic-anoxic process for treating low COD/N tropical wastewater: Startup, optimization and nitrifying community structure

How SW, Nittami T, Ngoh GC, Curtis TP, Chua ASM

Chemosphere, 2020 Nov;259:127444.
PMID: 32640378 DOI: 10.1016/j.chemosphere.2020.127444

In this study, we assessed and optimized a low-dissolved-oxygen oxic-anoxic (low-DO OA) process to achieve a low-cost and sustainable solution for wastewater treatment systems in the developing tropical countries treating low chemical oxygen demand-to-nitrogen ratio (COD/N) wastewater. The low-DO OA process attained complete ammonia removal and the effluent nitrate nitrogen (NO3-N) was below 0.3 mg/L. The recommended hydraulic retention time and sludge retention time (SRT) were 16 h and 20 days, respectively. The 16S rRNA sequencing data revealed that long SRT (20 days) encouraged the growth of nitrite-oxidizing bacteria (NOB) affiliated with "Candidatus Nitrospira defluvii". Comammox made up 10-20% of the Nitrospira community. NOB and comammox related to Nitrospira were enriched at long SRT (20 days) to achieve good low-DO nitrification performance. The low-DO OA process was efficient and has simpler design than conventional processes, which are keys for sustainable wastewater treatment systems in the developing countries treating low COD/N wastewater.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Review of clinical aspects, epidemiology and diagnosis of haemotropic Mycoplasma ovis in small ruminants: current status and future perspectives in tropics focusing on Malaysia

Paul BT, Jesse FFA, Chung ELT, Che-Amat A, Mohd Lila MA, Hashi HA, et al.

Trop Anim Health Prod, 2020 Nov;52(6):2829-2844.
PMID: 32712811 DOI: 10.1007/s11250-020-02357-9

Mycoplasma ovis (formerly Eperythrozoon ovis) is an epierythrocytic parasitic bacterium of small ruminants known as haemotropic mycoplasma, which is transmitted mechanically by biting flies and contaminated instruments. Acute mycoplasmosis causes severe haemolytic anaemia and mortality in young animals. At the same time, chronic disease may produce mild anaemia and varying degrees of morbidity depending on several factors, including age, reproductive status, the plane of nutrition, immunological status and the presence of concurrent infection. Haemotropic Mycoplasma ovis is currently recognised as an emerging zoonotic pathogen which is widely distributed in the sheep and goat producing areas of tropics and subtropics, where the disease is nearly endemic. Human infection has been reported in pregnant women, immunocompromised patients and people exposed to animals and arthropods. The current diagnosis of haemoplasma relies on microscopic evaluation of Giemsa-stained blood smear and PCR. Although there are few published reports on the incidence of haemotropic Mycoplasma ovis infection of small ruminants in Malaysia, information on its prevalence, risk factors, severity and economic impacts is grossly inadequate. Therefore, a large-scale survey of small ruminant flocks is necessary to elucidate the current seroprevalence status and molecular characteristics of haemotropic M. ovis infection in Malaysia using ELISA and PCR sequencing technologies. In the future, surveillance programs, including vector forecast, quarantine, monitoring by periodic surveys and public enlightenment, will limit the internal and transboundary spread of M. ovis, enhance control efforts and mitigate production losses in Malaysia.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Inhibition of Quorum Sensing and Biofilm Formation in Chromobacterium violaceum by Fruit Extracts of Passiflora edulis

Venkatramanan M, Sankar Ganesh P, Senthil R, Akshay J, Veera Ravi A, Langeswaran K, et al.

ACS Omega, 2020 Oct 13;5(40):25605-25616.
PMID: 33073086 DOI: 10.1021/acsomega.0c02483

Chromobacterium violaceum (C. violaceum) is a Gram-negative, rod-shaped facultatively anaerobic bacterium implicated with recalcitrant human infections. Here, we evaluated the anti-QS and antibiofilm activities of ethyl acetate extracts of Passiflora edulis (P. edulis) on the likely inactivation of acyl-homoserine lactone (AHL)-regulated molecules in C. violaceum both by in vitro and in silico analyses. Our investigations showed that the sub-MIC levels were 2, 1, and 0.5 mg/mL, and the concentrations showed a marked reduction in violacein pigment production by 75.8, 64.6, and 35.2%. AHL quantification showed 72.5, 52.2, and 35.9% inhibitions, inhibitions of EPS production (72.8, 36.5, and 25.9%), and reductions in biofilm formation (90.7, 69.4, and 51.8%) as compared to a control. Light microscopy and CLSM analysis revealed dramatic reduction in the treated biofilm group as compared to the control. GC-MS analysis showed 20 major peaks whose chemical structures were docked as the CviR ligand. The highest docking score was observed for hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester bonds in the active site of CviR with a binding energy of -8.825 kcal/mol. Together, we found that hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester remarkably interacted with CviR to inhibit the QS system. Hence, we concluded that hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester of P. edulis could likely be evaluated for treating C. violaceum infections.

Matched MeSH terms: RNA, Ribosomal, 16S
Molecular evidence of Anaplasma infection in naturally affected domestic cats of Pakistan

Ahmed A, Ijaz M, Ghauri HN, Aziz MU, Ghaffar A, Naveed M, et al.

Comp Immunol Microbiol Infect Dis, 2020 Oct;72:101524.
PMID: 32829184 DOI: 10.1016/j.cimid.2020.101524

Feline anaplasmosis is considered as an emerging tick-borne disease of zoonotic potential. The aim of current study was to investigate the molecular prevalence of anaplasmosis, associated risk factors, and alterations in hematological parameters of domestic cats from Lahore, Pakistan. Blood samples of 100 domestic cats from district Lahore were examined microscopically and the extracted genomic DNA from each sample was processed for the amplification of 16 S rRNA gene of Anaplasma. PCR confirmed isolates were purified for sequencing. The data regarding the risk factors was collected in a predesigned questionnaire and statistically analyzed by logistic regression analysis. The study found a molecular prevalence of 13% (13/100) among analyzed blood samples. The nucleotide analysis of Anaplasmataceae species sequences amplified by PCR showed high resemblance (99%) with isolates from Korea, Japan, Malaysia, Philippines, and India. The potential risk factors found to be significantly associated (p 

Matched MeSH terms: RNA, Ribosomal, 16S/genetics

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