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BMC Genomics Jun 2019Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety...
BACKGROUND
Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes.
RESULTS
Genome sequencing, assembly, and annotation of both strains delineate stark patterns of genomic erosion and sequence divergence in gut associated AAB. We found widespread horizontal gene transfer (HGT) in these bacterial associates and report elevated gene acquisition associated with energy production and conversion, amino acid and coenzyme transport and metabolism, defense mechanisms, and lysine export. Both strains have acquired the complete NADH-quinone oxidoreductase complex, plausibly from an Enterobacteriaceae origin, likely facilitating energy production under diverse conditions. Conservation of several lysine biosynthetic and salvage pathways and accumulation of lysine export genes via HGT implicate L-lysine supplementation by both strains as a potential functional benefit for the host. These trends are contrasted by genome-wide erosion of several amino acid biosynthetic pathways and pathways in central metabolism. We perform phylogenomic analyses on both strains as well as several free living and host associated AAB. Based on their monophyly and deep divergence from other AAB, these C. chromaiodes gut associates may represent a novel genus. Together, our results demonstrate how extensive horizontal transfer between gut associates along with genome-wide deletions leads to mosaic metabolic pathways. More broadly, these patterns demonstrate that HGT and genomic erosion shape metabolic capabilities of persistent gut associates and influence their genomic evolution.
CONCLUSIONS
Using comparative genomics, our study reveals substantial changes in genomic content in persistent associates of the insect gastrointestinal tract and provides evidence for the evolutionary pressures inherent to this environment. We describe patterns of genomic erosion and horizontal acquisition that result in mosaic metabolic pathways. Accordingly, the phylogenetic position of both strains of these associates form a divergent, monophyletic clade sister to gut associates of honey bees and more distantly to Gluconobacter.
Topics: Acetobacteraceae; Animals; Ants; Evolution, Molecular; Gastrointestinal Tract; Gene Transfer, Horizontal; Genomics; Metabolic Networks and Pathways; Phylogeny; Symbiosis
PubMed: 31182035
DOI: 10.1186/s12864-019-5844-5 -
Biotechnology Advances Sep 2022Acetic acid bacteria (AAB) are a group of gram-negative, obligate aerobic bacteria within the Acetobacteraceae family of the alphaproteobacteria class, which are... (Review)
Review
Acetic acid bacteria (AAB) are a group of gram-negative, obligate aerobic bacteria within the Acetobacteraceae family of the alphaproteobacteria class, which are distributed in a wide variety of different natural sources that are rich in sugar and alcohols, as well as in several traditionally fermented foods. Their versatile capabilities are not limited to producing acetic acid and brewing vinegar, as their names suggest. They can also be used for fixing nitrogen, yielding pigments and exopolysaccharides (EPS), and most typically, producing a variety of aldehydes, ketones and other organic acids from the incomplete oxidation of the corresponding alcohols and/or sugars (also referred to as oxidative fermentation). In order to gain more insight into these organisms, molecular biology techniques have been extensively applied in almost all aspects of AAB research, including their identification and classification, acid resistance mechanisms, oxidative fermentation, EPS production, thermotolerance and so on. In this review, we mainly focus on the application of molecular biological technologies in the advancement of research into AAB while presenting the progress of the latest studies using these techniques.
Topics: Acetic Acid; Acetobacteraceae; Alcohols; Fermentation; Molecular Biology
PubMed: 35033586
DOI: 10.1016/j.biotechadv.2022.107911 -
Bioscience, Biotechnology, and... 2016Environmental adaptation is considered as one of the most challenging subjects in biology to understand evolutionary or ecological diversification processes and in... (Review)
Review
Environmental adaptation is considered as one of the most challenging subjects in biology to understand evolutionary or ecological diversification processes and in biotechnology to obtain useful microbial strains. Temperature is one of the important environmental stresses; however, microbial adaptation to higher temperatures has not been studied extensively. For industrial purposes, the use of thermally adapted strains is important, not only to reduce the cooling expenses of the fermentation system, but also to protect fermentation production from accidental failure of thermal management. Recent progress in next-generation sequencing provides a powerful tool to track the genomic changes of the adapted strains and allows us to compare genomic DNA sequences of conventional strains with those of their closely related thermotolerant strains. In this article, we have attempted to summarize our recent approaches to produce thermotolerant strains by thermal adaptation and comparative genomic analyses of Acetobacter pasteurianus for high-temperature acetic acid fermentations, and Zymomonas mobilis and Kluyveromyces marxianus for high-temperature ethanol fermentations. Genomic analysis of the adapted strains has found a large number of mutations and/or disruptions in highly diversified genes, which could be categorized into groups related to cell surface functions, ion or amino acid transporters, and some transcriptional factors. Furthermore, several phenotypic and genetic analyses revealed that the thermal adaptation could lead to decreased ROS generation in cells that produce higher ROS levels at higher temperatures. Thus, it is suggested that the thermally adapted cells could become robust and resistant to many stressors, and thus could be useful for high-temperature fermentations.
Topics: Acetic Acid; Acetobacter; Adaptation, Physiological; DNA Transposable Elements; Fermentation; Genome, Bacterial; Genome, Fungal; Hot Temperature; Kluyveromyces
PubMed: 26566045
DOI: 10.1080/09168451.2015.1104235 -
International Journal of Systematic and... Nov 2020Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569, were isolated...
Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569, were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569 belong to the family and the most closely related species are (96.1 %), (95.9 %) and (95.7 %). Phylogenomic and genomic relatedness analyses showed that strains PAMC 26568 and PAMC 26569 are clearly distinguished from other genera in the family by average nucleotide identity values (<72.8 %) and the genome-to-genome distance values (<22.5 %). Genomic analysis revealed that strains PAMC 26568 and PAMC 26569 do not contain genes involved in atmospheric nitrogen fixation and utilization of sole carbon compounds such as methane and methanol. Instead, strains PAMC 26568 and PAMC 26569 possess genes to utilize nitrate and nitrite and certain monosaccharides and disaccharides. The major fatty acids (>10 %) are summed feature 8 (C ω7 and/or C ω6; 40.3-40.4 %), C 2OH (22.7-23.7 %) and summed feature 2 (C 3OH and/or C iso I; 12.0 % in PAMC 26568). The major respiratory quinone is Q-10. The genomic DNA G+C content of PAMC 26568 and PAMC 26569 is 64.6 %. Their distinct phylogenetic position and some physiological characteristics distinguish strains PAMC 26568 and PAMC 26569 from other genera in the family supporting the proposal of gen. nov., with the type species sp. nov. (type strain, PAMC 26569=KCCM 43315=JCM 33604).
Topics: Acetobacteraceae; Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lichens; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone
PubMed: 33034550
DOI: 10.1099/ijsem.0.004495 -
BMC Microbiology Jul 2016Symbiotic associations between gut microbiota and their animal hosts shape the evolutionary trajectories of both partners. The genomic consequences of these...
BACKGROUND
Symbiotic associations between gut microbiota and their animal hosts shape the evolutionary trajectories of both partners. The genomic consequences of these relationships are significantly influenced by a variety of factors, including niche localization, interaction potential, and symbiont transmission mode. In eusocial insect hosts, socially transmitted gut microbiota may represent an intermediate point between free living or environmentally acquired bacteria and those with strict host association and maternal transmission.
RESULTS
We characterized the bacterial communities associated with an abundant ant species, Camponotus chromaiodes. While many bacteria had sporadic distributions, some taxa were abundant and persistent within and across ant colonies. Specially, two Acetobacteraceae operational taxonomic units (OTUs; referred to as AAB1 and AAB2) were abundant and widespread across host samples. Dissection experiments confirmed that AAB1 and AAB2 occur in C. chromaiodes gut tracts. We explored the distribution and evolution of these Acetobacteraceae OTUs in more depth. We found that Camponotus hosts representing different species and geographical regions possess close relatives of the Acetobacteraceae OTUs detected in C. chromaiodes. Phylogenetic analysis revealed that AAB1 and AAB2 join other ant associates in a monophyletic clade. This clade consists of Acetobacteraceae from three ant tribes, including a third, basal lineage associated with Attine ants. This ant-specific AAB clade exhibits a significant acceleration of substitution rates at the 16S rDNA gene and elevated AT content. Substitutions along 16S rRNA in AAB1 and AAB2 result in ~10 % reduction in the predicted rRNA stability.
CONCLUSIONS
Combined, these patterns in Camponotus-associated Acetobacteraceae resemble those found in cospeciating gut associates that are both socially and maternally transmitted. These associates may represent an intermediate point along an evolutionary trajectory manifest most extremely in symbionts with strict maternal transmission. Collectively, these results suggest that Acetobacteraceae may be a frequent and persistent gut associate in Camponotus species and perhaps other ant groups, and that its evolution is strongly impacted by this host association.
Topics: Acetobacteraceae; Animals; Ants; Base Sequence; Biodiversity; Biological Evolution; DNA, Bacterial; DNA, Ribosomal; Evolution, Molecular; Gastrointestinal Microbiome; Genes, Bacterial; Host Specificity; Microbial Consortia; Phylogeny; RNA, Ribosomal, 16S; Sequence Alignment; Sequence Analysis, DNA; Symbiosis
PubMed: 27400652
DOI: 10.1186/s12866-016-0721-8 -
World Journal of Microbiology &... Jun 2022Gluconobacter oxydans is a well-known acetic acid bacterium that has long been applied in the biotechnological industry. Its extraordinary capacity to oxidize a variety... (Review)
Review
Gluconobacter oxydans is a well-known acetic acid bacterium that has long been applied in the biotechnological industry. Its extraordinary capacity to oxidize a variety of sugars, polyols, and alcohols into acids, aldehydes, and ketones is advantageous for the production of valuable compounds. Relevant G. oxydans industrial applications are in the manufacture of L-ascorbic acid (vitamin C), miglitol, gluconic acid and its derivatives, and dihydroxyacetone. Increasing efforts on improving these processes have been made in the last few years, especially by applying metabolic engineering. Thereby, a series of genes have been targeted to construct powerful recombinant strains to be used in optimized fermentation. Furthermore, low-cost feedstocks, mostly agro-industrial wastes or byproducts, have been investigated, to reduce processing costs and improve the sustainability of G. oxydans bioprocess. Nonetheless, further research is required mainly to make these raw materials feasible at the industrial scale. The current shortage of suitable genetic tools for metabolic engineering modifications in G. oxydans is another challenge to be overcome. This paper aims to give an overview of the most relevant industrial G. oxydans processes and the current strategies developed for their improvement.
Topics: Acetic Acid; Biotechnology; Fermentation; Gluconobacter oxydans; Metabolic Engineering
PubMed: 35688964
DOI: 10.1007/s11274-022-03310-8 -
Bioscience, Biotechnology, and... Apr 2024Gluconobacter strains perform incomplete oxidation of various sugars and alcohols, employing regio- and stereoselective membrane-bound dehydrogenases oriented toward the... (Review)
Review
Gluconobacter strains perform incomplete oxidation of various sugars and alcohols, employing regio- and stereoselective membrane-bound dehydrogenases oriented toward the periplasmic space. This oxidative fermentation process is utilized industrially. The ketogluconate production pathway, characteristic of these strains, begins with the conversion of d-glucose to d-gluconate, which then diverges and splits into 2 pathways producing 5-keto-d-gluconate and 2-keto-d-gluconate and subsequently 2,5-diketo-d-gluconate. These transformations are facilitated by membrane-bound d-glucose dehydrogenase, glycerol dehydrogenase, d-gluconate dehydrogenase, and 2-keto-d-gluconate dehydrogenase. The variance in end products across Gluconobacter strains stems from the diversity of enzymes and their activities. This review synthesizes biochemical and genetic knowledge with biotechnological applications, highlighting recent advances in metabolic engineering and the development of an efficient production process focusing on enzymes relevant to the ketogluconate production pathway in Gluconobacter strains.
Topics: Gluconates; Gluconobacter; Biotechnology; Fermentation; Metabolic Engineering; Glucose; Glucose 1-Dehydrogenase; Sugar Alcohol Dehydrogenases
PubMed: 38323387
DOI: 10.1093/bbb/zbae013 -
Biotechnology and Bioengineering Aug 2019Adaptive laboratory evolution through 12 rounds of culturing experiments of the nanocellulose-producing bacterium Komagataeibacter hansenii ATCC 23769 in a liquid...
Adaptive laboratory evolution through 12 rounds of culturing experiments of the nanocellulose-producing bacterium Komagataeibacter hansenii ATCC 23769 in a liquid fraction from hydrothermal pretreatment of corn stover resulted in a strain that resists inhibition by phenolics. The original strain generated nanocellulose from glucose in standard Hestrin and Schramm (HS) medium, but not from the glucose in pretreatment liquid. K. hansenii cultured in pretreatment liquid treated with activated charcoal to remove inhibitors also converted glucose to bacterial nanocellulose and used xylose as carbon source for growth. The properties of this cellulose were the same as nanocellulose generated from media specifically formulated for bacterial cellulose formation. However, attempts to directly utilize glucose proved unsuccessful due to the toxic character of the lignin-derived phenolics, and in particular, vanillan and ferulic acid. Adaptive laboratory evolution at increasing concentrations of pretreatment liquid from corn stover in HS medium resulted in a strain of K. hansenii that generated bacterial nanocellulose directly from pretreatment liquids of corn stover. The development of this adapted strain positions pretreatment liquid as a valuable resource since K. hansenii is able to convert and thereby concentrate a dilute form of glucose into an insoluble, readily recovered and value-added product-bacterial nanocellulose.
Topics: Acetobacteraceae; Cellulose; Glucose; Industrial Microbiology; Lignin; Polysaccharides, Bacterial; Zea mays
PubMed: 31038201
DOI: 10.1002/bit.26997 -
International Journal of Systematic and... Aug 2020Gram-negative, aerobic, chemo-organotrophic and bacteriochlorophyll -containing bacterial strains, KEBCLARHB70R, KAMCLST3051 and KAMCLST3152, were isolated from the...
Gram-negative, aerobic, chemo-organotrophic and bacteriochlorophyll -containing bacterial strains, KEBCLARHB70R, KAMCLST3051 and KAMCLST3152, were isolated from the thalli of and lichens. Cells from the strains were coccoid and reproduced by binary division. They were motile at the early stages of growth and utilized sugars and alcohols. All strains were psychrophilic and acidophilic, capable of growth between pH 3.5 and 7.5 (optimum, pH 5.5), and at 4-30 °C (optimum, 10-15 °C). The major fatty acids were C ω7 and C; the lipids were phosphatidylcholines, phosphatidylethanolamines, phosphatidic acids, phosphatidylglycerol, glycolipids, diphosphatidylglycerol and polar lipids with an unknown structure. The quinone was Q-10. The DNA G+C content was 67.8 mol%. Comparative 16S rRNA gene analysis together with other data, supported that the strains, KEBCLARHB70R, KAMCLST3051 and KAMCLST3152 belonged to the same species. Whole genome analysis of the strain KEBCLARHB70R and average amino acid identity values confirmed its distinctive phylogenetic position within the family . Phenotypic, ecological and genomic characteristics distinguished strains KEBCLARHB70R, KAMCLST3051 and KAMCLST3152 from all genera in the family . Therefore, we propose a novel genus and a novel species, gen. nov., sp. nov., for these novel members. Strain KEBCLARHB70R (=KCTC 72321=VKM B-3305) has been designated as the type strain.
Topics: Acetobacteraceae; Bacterial Typing Techniques; Bacteriochlorophyll A; Base Composition; DNA, Bacterial; Fatty Acids; Glycolipids; Lichens; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Russia; Sequence Analysis, DNA; Ubiquinone
PubMed: 32658637
DOI: 10.1099/ijsem.0.004318 -
Scientific Reports May 2023Several raw materials have been used as partial supplements or entire replacements for the main ingredients of kombucha to improve the biological properties of the...
Several raw materials have been used as partial supplements or entire replacements for the main ingredients of kombucha to improve the biological properties of the resulting kombucha beverage. This study used pineapple peels and cores (PPC), byproducts of pineapple processing, as alternative raw materials instead of sugar for kombucha production. Kombuchas were produced from fusions of black tea and PPC at different ratios, and their chemical profiles and biological properties, including antioxidant and antimicrobial activities, were determined and compared with the control kombucha without PPC supplementation. The results showed that PPC contained high amounts of beneficial substances, including sugars, polyphenols, organic acids, vitamins, and minerals. An analysis of the microbial community in a kombucha SCOBY (Symbiotic Cultures of Bacteria and Yeasts) using next-generation sequencing revealed that Acetobacter and Komagataeibacter were the most predominant acetic acid bacteria. Furthermore, Dekkera and Bacillus were also the prominent yeast and bacteria in the kombucha SCOBY. A comparative analysis was performed for kombucha products fermented using black tea and a fusion of black tea and PPC, and the results revealed that the kombucha made from the black tea and PPC infusion exhibited a higher total phenolic content and antioxidant activity than the control kombucha. The antimicrobial properties of the kombucha products made from black tea and the PPC infusion were also greater than those of the control. Several volatile compounds that contributed to the flavor, aroma, and beneficial health properties, such as esters, carboxylic acids, phenols, alcohols, aldehydes, and ketones, were detected in kombucha products made from a fusion of black tea and PPC. This study shows that PPC exhibits high potential as a supplement to the raw material infusion used with black tea for functional kombucha production.
Topics: Tea; Ananas; Beverages; Yeasts; Antioxidants; Camellia sinensis; Phenols; Anti-Infective Agents; Acetobacteraceae; Fermentation
PubMed: 37188725
DOI: 10.1038/s41598-023-34954-7