Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu

From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees

For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.

Analysis of differences in microorganisms and aroma profiles between normal and off-flavor pit mud in Chinese strong-flavor Baijiu

The unique cellar fermentation process of Chinese strong-flavor Baijiu is the reason for its characteristic cellar aroma flavor. The types, abundance, community structure and metabolic activity of microorganisms in the pit mud directly affect the microbial balance in the white spirit production environment, promoting the formation of typical aromas and influencing the quality of CFSB. During the production process, the production of off-flavor in the cellar may occur. The aim of this study is to elucidate the differences in microbiota and flavor between normal pit mud and abnormal pit mud (pit mud with off-flavor). A total of 46 major volatile compounds were identified, and 24 bacterial genera and 21 fungal genera were screened. The esters, acids, and alcohols in the abnormal pit mud were lower than those in the normal pit mud, while the aldehydes were higher. 3-Methyl indole, which has been proven to be responsible for the muddy and musty flavors, was detected in both types of pit mud, and for the first time, high levels of 4-methylanisole was detected in the pit mud. The microbial composition of the two types of pit mud showed significant differences in the bacterial genera of Sporosarcina, Lactobacillus, Garciella, Anaerosalibacter, Lentimicrobium, HN-HF0106, Petrimonas, Clostridium_sensu_stricto_12 and Bacillus, and the fungal genera of Millerozyma, Penicillium, Mortierella, Monascus, Saccharomyces, Issatchenkia, Pithoascus, Pseudallescheria, and Wickerhamomyces. Additionally, we speculate that Sporosarcina is the predominant bacterial genus responsible for the imbalance of microbiota in pit mud.

Systematic Review of Actinomycetes in the Baijiu Fermentation Microbiome

Actinomycetes (a group of filamentous bacteria) are the dominant microbial order in the Daqu (DQ) fermentation starter and in the pit mud (PM) of the Baijiu fermentation microbiome. Actinomycetes produce many of the key enzymes and flavor components, and supply important precursors, which have a major influence on its characteristic aroma components, to other microorganisms during fermentation. This paper reviews the current progress on actinomycete research related to Baijiu fermentation, including the isolation and identification, distribution, interspecies interactions, systems biology, and main metabolites. The main metabolites and applications of the actinomycetes during Baijiu fermentation are also discussed.

Shewanella shenzhenensis sp. nov., a novel Fe(III)-reducing bacterium with abundant possible cytochrome genes, isolated from mangrove sediment

A facultative anaerobic bacterium, designated as A25^T, was isolated from a mangrove sediment sample collected in Shenzhen, China. Cells of strain A25^T were found to be Gram-staining negative, rod-shaped, flagella-harboring, and oxidase- and catalase-positive. The isolate was able to grow at 4-40 °C (optimum 28 °C) and pH 5.0-9.0 (optimum pH 6.0), and in 0-10% NaCl concentration (w/v) (optimum 1%). Strain A25^T was capable of reducing Fe(III) citrate under anaerobic conditions. The major fatty acids of this strain was C_16:1ω7c/C_16:1ω6c (summed feature 3), C_17:1ω8c and iso-C_15:0. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain A25^T is affiliated with the genus Shewanella, showing the highest similarity to Shewanella seohaensis S7-3^T (98.4% similarity). The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain A25^T and its closely related strains were ≤ 79.0% and ≤ 22.8%, respectively. Based on its phenotypic, phylogenetic properties and physiological and biochemical characteristics, strain A25^T (= JCM 34900^T = GDMCC 1.2731^T) was designated as the type strain of a novel species of the genus Shewanella, for which the name Shewanella shenzhenensis sp. nov. was proposed.

Olsenella intestinalis sp. nov., isolated from cow feces

A Gram-stain-negative, anaerobic, non-motile, rod-shaped bacterium, designated as BGYT1^T, was isolated from the feces of a cow in Andong, Republic of Korea. It was studied using a polyphasic method to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BGYT1^T formed a lineage within the genus Olsenella and was most closely related to O. umbonate KCTC 15140^T (98.2%). The complete genome sequence of strain BGYT1^T was 2,476,083 bp long with a G + C content of 66.9 mol% and contained 1835 genes and 8 contigs. The N50 value was 604,117 bp. There were 50 tRNAs, 6 rRNAs (5S, 16S, 23S), 1778 CDSs and 2 BGCs and 1 tmRNA. The values for ANI (76.8%), AAI (67.3%), and dDDH (22.2%) compared to the closest related species were all below the threshold for bacterial species delineation. In addition, genes encoding the cell wall degrading enzymes such as chitinases, β-1,3 glucanases, and proteases were also detected. The strain was able to grow at pH 6.0-8.0 (optimum, pH 7.0), in the presence of 0.5-1.5% NaCl (optimum, 0.5%, w/v) and at the temperature range of 35-40 °C (optimum, 35 °C). The predominant fatty acids were C_16:0 DMA (20.2%), C_16:0 (20.2%), C_18:0 (10.5%) and C_18:1 cis 9 (17.0%). The polar lipids consisted of an unidentified phospholipid, four unidentified glycolipids and three unidentified lipids. Based on its phenotypic analyses, phylogenetic and physiological characteristics, strain BGYT1^T represented a novel species within the genus Olsenella, for which the name Olsenella intestinalis sp. nov. is proposed. The type strain is BGYT1^T (= KCTC 25379^T = GDMCC 1.3011^T).

Shewanella jiangmenensis sp. nov., isolated from aquaculture water

A Gram-stain-negative and facultatively anaerobic bacterial strain designated as JM162201^T was isolated from aquaculture water for farming Pacific white shrimp (Litopenaeus vannamei). The genome size of strain JM162201^T was 4,436,316 bp, and the genomic DNA G + C content was 55.0%. Phylogenetic analysis based on 16S rRNA gene sequences and genomes showed that strain JM162201^T belonged to the genus Shewanella and was closely related to Shewanella litorisediminis SMK1-12^T (97.1%), Shewanella khirikhana TH2012^T (97.0%), and Shewanella amazonensis SB2B^T (96.0%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain JM162201^T and three reference type strains were below the recognized thresholds of 95.0-96.0% (for ANI) and 70.0% (for dDDH) for species delineation. Growth occurred at 10-40 °C (optimum, 30 °C), at pH 4.0-10.0 (optimum, 7.0-8.0), and in 0-6.0% NaCl (w/v, optimum, 0-0.1%). The major cellular fatty acids of strain JM162201^T were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), C_17:1 ω8c, iso-C_15:0, C_16:0, and C_15:0. The predominant quinones were MK7, Q-7, and Q-8. The major polar lipids were phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Based on the polyphasic taxonomical analyses, strain JM162201^T represents a novel species of the genus Shewanella, for which the name Shewanella jiangmenensis sp. nov. is proposed, with the type strain JM162201^T (= GDMCC 1.2006^T = KCTC 82340^T).