Termotolerant Komagataeibacter melomenusus AAB2’nin karşılaştırmalı filogenetik ve tüm genoma dayalı identifikasyonu ile karbonhidrat aktif enzimlerinin in silico analizi

Öz

Ana bileşeni asetik asit olan sirke ve ilgili biyoürünler, organoleptik özellikleri ve sağlık üzerindeki olumlu etkileri nedeniyle başta Avrupa ve Asya olmak üzere dünya genelinde yaygın olarak tüketilen gıda maddeleri arasında yer almaktadır.  Artan fonksiyonel gıda talebi ve sürdürülebilir biyoproses arayışları, asetik asit bakterilerinin genomik düzeyde daha derinlemesine karakterizasyonunu gerekli kılmaktadır. Endüstriyel ölçekte asetik asit üretimi, ağırlıklı olarak Acetobacter ve Komagataeibacter cinslerine dayanmaktadır. Bu çalışmada, daha önce elma sirkesinden izole edilen termotolerant bir asetik asit bakterisi olan Komagataeibacter sp. AAB2 suşunun tüm genom dizilimi gerçekleştirilmiş, genotaksonomik konumu belirlenmiştir. Suşun potansiyel endüstriyel uygulamalarını incelemek amacıyla karbonhidrat-aktif enzim (CAZyme) profili analiz edilmiştir. 16S rRNA gen dizisi analizleri, AAB2’nin K. nataicola ile %98,90, recA aminoasit dizisi analizleri ise K. medellinensis ile %99,42 oranında homoloji gösterdiğini ortaya koymuştur. Illumina NovaSeq 6000 platformu ile elde edilen genom verisine göre, AAB2’nin genom uzunluğu 3.471.305 baz çifti olup, tüm genom analizleri sonucunda elde edilen ortalama nükleotid benzerliği (ANI) %99,01 ve dijital DNA-DNA hibridizasyon (dDDH) skoru %91,10 olarak bulunmuştur. Bu veriler, AAB2 suşunun K. melomenusus türüne ait olduğunu güçlü biçimde desteklemektedir. Fonksiyonel anotasyon sonucunda toplam 69 CAZyme kodlayan gen tanımlanmış olup, bunların büyük çoğunluğu glikoziltransferazlar (GT) ve glikozit hidrolazlar (GH) sınıfına aittir. Ayrıca karbonhidrat esterazları (CE), yardımcı aktiviteler (AA) ve karbonhidrat bağlayıcı modüller (CBM) ile ilişkili genler de tespit edilmiştir. Bu bulgular, AAB2 suşunun karbonhidrat metabolizmasının geniş bir genetik kapasiteye sahip olduğunu ve potansiyel biyoteknolojik uygulamalar için değerli bir kaynak olabileceğini işaret etmektedir. Sonuç olarak, genomik ve diğer omik tabanlı yaklaşımlar, asetik asit bakterilerinin hem tür düzeyinde taksonomik sınıflandırılmasında hem de fermentatif kapasitelerinin değerlendirilmesinde altın standart olarak önemini sürdürmektedir.

Anahtar Kelimeler

• Komagataeibacter spp.
• termotolerant AAB
• Filogenomik analiz
• CAZymes

Comparative phylogenetic and whole-genome-based identification of thermotolerant Komagataeibacter melomenusus AAB2 and in silico analysis of carbohydrate-active enzymes

Öz

Vinegar and related bio-products, whose main component is acetic acid, are widely consumed worldwide, particularly in Europe and Asia, due to their organoleptic properties and health-promoting effects. Increasing demand for functional foods and the pursuit of sustainable bioprocesses necessitate a more in-depth genomic characterization of acetic acid bacteria. Industrial production of acetic acid primarily relies on bacteria of the Acetobacter and Komagataeibacter genera. In this study, the complete genome of a thermotolerant acetic acid bacterium, Komagataeibacter sp. AAB2, previously isolated from apple vinegar, was sequenced, its genotaxonomic position was determined, and its carbohydrate-active enzyme (CAZyme) profile was analyzed to evaluate its potential industrial applications. Analysis of the 16S rRNA gene indicated 98.90% homology with K. nataicola, whereas recA amino acid sequence analysis revealed 99.42% similarity with K. medellinensis. Genome sequencing on the Illumina NovaSeq 6000 platform revealed that AAB2 has a genome of 3,471,305 base pairs. Comparative genomic analyses yielded an average nucleotide identity (ANI) of 99.01% and a digital DNA-DNA hybridization (dDDH) score of 91.10%, strongly supporting the classification of AAB2 as K. melomenusus. Functional annotation identified 69 CAZyme-encoding genes, predominantly glycosyltransferases (GT) and glycoside hydrolases (GH), with additional genes associated with carbohydrate esterases (CE), auxiliary activities (AA), and carbohydrate-binding modules (CBM). These findings indicate that AAB2 harbors a diverse genetic capacity for carbohydrate metabolism and represents a valuable resource for potential biotechnological applications. In conclusion, genomic and other omics-based approaches continue to serve as the gold standard for both species-level taxonomic classification and evaluation of fermentative capabilities in acetic acid bacteria.

Anahtar Kelimeler

• Komagataeibacter spp.
• thermotolerant AAB
• Phylogenomic analysis
• CAZymes

Kaynakça

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