Molecular biology: Fantastic toolkits to improve knowledge and application of acetic acid bacteria

Yang, Haoran; Chen, Tao; Wang, Min; Zhou, Jingwen; Liebl, Wolfgang; Barja, François; Chen, Fusheng

doi:10.1016/j.biotechadv.2022.107911

Cited by 20 publications

(19 citation statements)

References 124 publications

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“…In recent decades, a lot of molecular biology techniques have been applied to investigate AOF, especially its mDHs. Hereinafter, we just make a brief introduction about the application of molecular biology technologies in AOF, especially the establishment of a marker-less gene deletion system, for more detailed information, please read our recent review article (Yang et al, 2022 ).…”

Section: Molecular Biological Methods For Aofmentioning

confidence: 99%

“…Subsequently, the clones with the vector integrated at either the upstream or downstream site of the target gene by the homologous recombination are screened by antibiotic resistance and will be used for the second homologous recombination, in which the clones without the vector will be obtained through the recombination of the other homologous flanking region and the counter selection marker. The second homologous recombination will yield either the wild type strain or the desired gene deletion mutant with the theoretical ratio of 1:1 (Yang et al, 2022 ).…”

Section: Molecular Biological Methods For Aofmentioning

confidence: 99%

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Oxidative Fermentation of Acetic Acid Bacteria and Its Products

Xie

Zhang

et al. 2022

Front. Microbiol.

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Acetic acid bacteria (AAB) are a group of Gram-negative, strictly aerobic bacteria, including 19 reported genera until 2021, which are widely found on the surface of flowers and fruits, or in traditionally fermented products. Many AAB strains have the great abilities to incompletely oxidize a large variety of carbohydrates, alcohols and related compounds to the corresponding products mainly including acetic acid, gluconic acid, gulonic acid, galactonic acid, sorbose, dihydroxyacetone and miglitol via the membrane-binding dehydrogenases, which is termed as AAB oxidative fermentation (AOF). Up to now, at least 86 AOF products have been reported in the literatures, but no any monograph or review of them has been published. In this review, at first, we briefly introduce the classification progress of AAB due to the rapid changes of AAB classification in recent years, then systematically describe the enzymes involved in AOF and classify the AOF products. Finally, we summarize the application of molecular biology technologies in AOF researches.

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Section: Molecular Biological Methods For Aofmentioning

confidence: 99%

Section: Molecular Biological Methods For Aofmentioning

confidence: 99%

Oxidative Fermentation of Acetic Acid Bacteria and Its Products

Xie

Zhang

et al. 2022

Front. Microbiol.

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“…Acetic acid bacteria (AAB), a group of Gram-negative and aerobic bacilli that can be isolated from flowers, fruits, soil, intestines, wine, and vinegar, are currently classified into 19 genera (Qiu et al, 2021 ). The Acetobacter, Gluconobacter , and Komagataeibacter species have been widely studied for their ability to efficiently oxidize ethanol to vinegar (Yang et al, 2022 ). However, abnormal vinegar fermentation is often observed, and the underlying mechanism remains unclear due to the complicated microbial community combined with uneven fermentation technology.…”

Section: Introductionmentioning

confidence: 99%

“…However, abnormal vinegar fermentation is often observed, and the underlying mechanism remains unclear due to the complicated microbial community combined with uneven fermentation technology. The multi-omics studies on traditional food fermentations have indicated the impacts conferred by the bacterial community fluctuation and the environmental conditions on the fermentation process (Das and Tamang, 2021 ; Ma et al, 2022 ; Yang et al, 2022 ; Zotta et al, 2022 ). In parallel, the recent findings of virome contributions to the evolution of bacterial communities rely on the ocean, soil, and gut metagenome investigations, which suggest the potential of phages in shaping the architecture and development of fermented food communities (Roy et al, 2020 ; Chevallereau et al, 2022 ; Ge et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, a Tectivirus- infecting Gluconobacter cerinus was isolated from wine musts (Philippe et al, 2018 ), and six temperate phages were obtained from Acetobacter pasteurianus (Omata et al, 2021 ). Furthermore, the available genomic data exhibit plenty of putative prophage loci in Acetobacter genomes, as well as in transposons, insertion sequences (ISs), and phage-associated genes, which are associated with some evolutionary and genetic advantages but also contribute to unstable genome features in Acetobacter (Yang et al, 2022 ). Recently, the available genomic data provide us a chance to comprehensively decipher the profile of Acetobacter prophage and its important role in physiology, evolution, and genetic diversity of Acetobacter .…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin–antitoxin system, and linkage with CRISPR-Cas system

Qian

Liang

et al. 2022

Front. Microbiol.

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Acetobacter is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with Acetobacter, including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in Acetobacter. Here, prophage prediction analysis using 148 available genomes from 34 Acetobacter species was carried out. In addition, the type II toxin–antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order Caudovirales dominated by the families Siphoviridae and Myroviridae prophages (71.4%). Notably, Acetobacter strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. Acetobacter prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in Acetobacter aceti, while the other Acetobacter species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of Acetobacter.

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