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Plasmid localization of sole rrn operon in genomes of Oecophyllibacter saccharovorans (Acetobacteraceae)

Chua KO, See-Too WS, Yong HS, Song SL, Yin WF, Chan KG

Plasmid, 2021 03;114:102559.
PMID: 33476637 DOI: 10.1016/j.plasmid.2021.102559

The bacterium Oecophyllibacter saccharovorans of family Acetobacteraceae is a symbiont of weaver ant Oecophylla smaragdina. In our previous study, we published the finding of novel O. saccharovorans strains Ha5T, Ta1 and Jb2 (Chua et al. 2020) but their plasmid sequences have not been reported before. Here, we demonstrate for the first time that the sole rrn operon of their genomes was detected on a 6.6 kb circular replicon. This replicon occurred in high copy number, much smaller size and lower G + C content than the main chromosome. Based on these features, the 6.6 kb circular replicon was regarded as rrn operon-containing plasmid. Further restriction analysis on the plasmids confirmed their circular conformation. A Southern hybridization analysis also corroborated the presence of 16S rRNA gene and thus the rrn operon on a single locus in the genome of the O. saccharovorans strains. However, similar genome architecture was not observed in other closely related bacterial strains. Additional survey also detected no plasmid-borne rrn operon in available genomes of validly described taxa of family Acetobacteraceae. To date, plasmid localization of rrn operon is rarely documented. This study reports the occurrence of rrn operon on the smallest bacterial plasmid in three O. saccharovorans strains and discusses its possible importance in enhancing their competitive fitness as bacterial symbiont of O. smaragdina.

Matched MeSH terms: Acetobacteraceae*
Whole genome sequencing analysis of Komagataeibacter nataicola reveals its potential in food waste valorisation for cellulose production

Nasharudin MIH, Siew SW, Ahmad HF, Mahmud N

Mol Biol Rep, 2024 Apr 11;51(1):503.
PMID: 38600404 DOI: 10.1007/s11033-024-09492-8

BACKGROUND: Komagataeibacter nataicola (K. nataicola) is a gram-negative acetic acid bacterium that produces natural bacterial cellulose (BC) as a fermentation product under acidic conditions. The goal of this work was to study the complete genome of K. nataicola and gain insight into the functional genes in K. nataicola that are responsible for BC synthesis in acidic environments.
METHODS AND RESULT: The pure culture of K. nataicola was obtained from yeast-glucose-calcium carbonate (YGC) agar, followed by genomic DNA extraction, and subjected to whole genome sequencing on a Nanopore flongle flow cell. The genome of K. nataicola consists of a 3,767,936 bp chromosome with six contigs and 4,557 protein coding sequences. The maximum likelihood phylogenetic tree and average nucleotide identity analysis confirmed that the bacterial isolate was K. nataicola. The gene annotation via RAST server discovered the presence of cellulose synthase, along with three genes associated with lactate utilization and eight genes involved in lactate fermentation that could potentially contribute to the increase in acid concentration during BC synthesis.
CONCLUSION: A more comprehensive genome study of K. nataicola may shed light into biological pathway in BC productivity as well as benefit the analysis of metabolites generated and understanding of biological and chemical interactions in BC production later.

Matched MeSH terms: Acetobacteraceae*
Fulltext Microbial Community Composition Reveals Spatial Variation and Distinctive Core Microbiome of the Weaver Ant Oecophylla smaragdina in Malaysia

Chua KO, Song SL, Yong HS, See-Too WS, Yin WF, Chan KG

Sci Rep, 2018 Jul 17;8(1):10777.
PMID: 30018403 DOI: 10.1038/s41598-018-29159-2

The weaver ant Oecophylla smaragdina is an aggressive predator of other arthropods and has been employed as a biological control agent against many insect pests in plantations. Despite playing important roles in pest management, information about the microbiota of O. smaragdina is limited. In this work, a number of O. smaragdina colonies (n = 12) from Malaysia had been studied on their microbiome profile using Illumina 16S rRNA gene amplicon sequencing. We characterized the core microbiota associated with these O. smaragdina and investigated variation between colonies from different environments. Across all 12 samples, 97.8% of the sequences were assigned to eight bacterial families and most communities were dominated by families Acetobacteraceae and Lactobacillaceae. Comparison among colonies revealed predominance of Acetobacteraceae in O. smaragdina from forest areas but reduced abundance was observed in colonies from urban areas. In addition, our findings also revealed distinctive community composition in O. smaragdina showing little taxonomic overlap with previously reported ant microbiota. In summary, our work provides information regarding microbiome of O. smaragdina which is essential for establishing healthy colonies. This study also forms the basis for further study on microbiome of O. smaragdina from other regions.

Matched MeSH terms: Acetobacteraceae/genetics; Acetobacteraceae/isolation & purification
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: Acetobacteraceae/classification*; Acetobacteraceae/genetics; Acetobacteraceae/isolation & purification*; Acetobacteraceae/physiology*
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: Acetobacteraceae
In vivo evaluation of bacterial cellulose/acrylic acid wound dressing hydrogel containing keratinocytes and fibroblasts for burn wounds

Mohamad N, Loh EYX, Fauzi MB, Ng MH, Mohd Amin MCI

Drug Deliv Transl Res, 2019 04;9(2):444-452.
PMID: 29302918 DOI: 10.1007/s13346-017-0475-3

The healing of wounds, including those from burns, currently exerts a burden on healthcare systems worldwide. Hydrogels are widely used as wound dressings and in the field of tissue engineering. The popularity of bacterial cellulose-based hydrogels has increased owing to their biocompatibility. Previous study demonstrated that bacterial cellulose/acrylic acid (BC/AA) hydrogel increased the healing rate of burn wound. This in vivo study using athymic mice has extended the use of BC/AA hydrogel by the addition of human epidermal keratinocytes and human dermal fibroblasts. The results showed that hydrogel loaded with cells produces the greatest acceleration on burn wound healing, followed by treatment with hydrogel alone, compared with the untreated group. The percentage wound reduction on day 13 in the mice treated with hydrogel loaded with cells (77.34 ± 6.21%) was significantly higher than that in the control-treated mice (64.79 ± 6.84%). Histological analysis, the expression of collagen type I via immunohistochemistry, and transmission electron microscopy indicated a greater deposition of collagen in the mice treated with hydrogel loaded with cells than in the mice administered other treatments. Therefore, the BC/AA hydrogel has promising application as a wound dressing and a cell carrier.

Matched MeSH terms: Acetobacteraceae