Updating the Relationship Between the Threshold Value of Average Nucleotide Identity and Digital DNA-DNA Hybridization for Reliable Taxonomy of Corynebacterium

Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.

Corynebacterium lipophilum sp. nov., a lipophilic bacterium isolated from clinical breast specimens and emended description of the species Corynebacterium pilbarense

Two isolates (MC-18T and MC-17D), representing the Gram-stain-positive, facultatively anaerobic, irregular rod-shaped, non-motile, and non-spore-forming actinobacteria, were isolated from clinical breast specimens in Guangzhou, China. The growth of the isolates is enhanced by supplementing 1% Tween-80 on Luria Bertani agar. Optimal growth of the isolates was observed at 37 °C, pH 7-8, and with 1% (w/v) NaCl on Columbia blood agar. Pairwise comparison of the 16S rRNA gene sequences revealed that isolates MC-18T and MC-17D shared the highest sequence similarities with Corynebacterium liangguodongii 2184T (96.9%), which were lower than the threshold value for species delineation (98.65%). Phylogenetic dendrograms based on the 16S rRNA gene, rpoB gene, and core genomes indicated that two isolates formed a distinct lineage within the genus Corynebacterium. The estimated dDDH, ANIb, ANIm, and AAI values between strain MC-18T and its closely related strains were below the threshold values generally considered for recognizing a new species. The genome DNA G + C contents of both the isolates MC-18T and MC-17D are 60.6%. The two isolates have virulence-related genes of the VF classes of adhesion and antiphagocytosis, and also contain the antimicrobial resistance genes ErmX, mtrA, rpoB2, and RbpA. The major fatty acids (> 10%) of isolates MC-18T and MC-17D were C16:0, C18:1 ω9c, C18:0 and summed feature 5 (anteiso-C18:0 and/or C18:2 ω6,9c). The main respiratory quinone of strain MC-18T was MK-8(H2), and the polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified glycolipids, an unidentified aminolipid, and four unidentified phosphoglycolipids. The two isolates lack mycolic acids in the cell envelope. Based on the above findings, the two isolates are considered to represent a novel species of the genus Corynebacterium, for which the name Corynebacterium lipophilum sp. nov. is proposed, with isolate MC-18T (= NBRC 115144T = CCTCC AB 2020201T) as the type strain. An emended description of the Corynebacterium pilbarense is also provided.

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov

Three novel corynebacterial species were isolated from soil sampled at a paddock in Vilsendorf, North Rhine-Westphalia, Germany. The strains were coccoid or irregular rod-shaped, catalase-positive and pale white to yellow-orange in colour. By whole genome sequencing and comparison of the 16S rRNA genes as well as the whole genome structure, it was shown that all three strains represent novel species of the family Corynebacteriaceae, order Corynebacteriales, class Actinobacteria. This project describes the isolation, identification, sequencing, and phenotypic characterization of the three novel Corynebacterium species. We propose the names Corynebacterium kalinowskii sp. nov. (DSM 110639^T=LMG 31801^T), Corynebacterium comes sp. nov. (DSM 110640^T=LMG 31802^T), and Corynebacterium occultum sp. nov. (DSM 110642^T=LMG 31803^T).

Chicken Gut Microbiome and Human Health: Past Scenarios, Current Perspectives, and Futuristic Applications

Sustainable poultry practices are needed to maintain an adequate supply of poultry products to the increasing human population without compromising human wellbeing. In order to achieve the understanding of the core microbiome that assumes an imperative role in digestion, absorption, and assimilation of feed as well as restrict the growth of pathogenic strains, a proper meta-data survey is required. The dysbiosis of the core microbiome or any external infection in chickens leads to huge losses in the poultry production worldwide. Along with this, the consumption of infected meat also impacts on human health as chicken meat is a regular staple in many diets as a vital source of protein. To tackle these losses, sub-therapeutic doses of antibiotics are being used as a feed additive along with other conventional approaches including selective breeding and modulation in feed composition. Altogether, these conventional approaches have improved the yield and quality of poultry products, however, the use of antibiotics encompasses the risk of developing multi-drug resistant pathogenic strains that can be harmful to human beings. Thus, there is an urgent need to understand the chicken microbiome in order to modulate chicken gut microbiome and provide alternatives to the conventional methods. Although there is now emerging literature available on some of these important microbiome aspects, in this article, we have analysed the relevant recent developments in understanding the chicken gut microbiome including the establishment of integrated gene catalogue for chicken microbiome. We have also focussed on novel strategies for the development of a chicken microbial library that can be used to develop novel microbial consortia as novel probiotics to improve the poultry meat production without compromising human health. Thus, it can be an alternative and advanced step compared to other conventional approaches to improve the gut milieu and pathogen-mediated loss in the poultry industry.

Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy

The present study reports the functional annotation of complete genome of methylotrophic bacterium Paracoccus sp. strain AK26. The 3.6 Mb genome with average GC content of 65.7% was distributed across five replicons; including chromosome (2.7 Mb) and four extrachromosomal replicons pAK1 (471Kb), pAK2 (189Kb), pAK3 (129Kb) and pAK4 (84 Kb). Interestingly, nearly 23% of the Cluster of Orthologous Group (COG) of proteins were annotated on extrachromosomal replicons and 185Kb genome content was attributed to segregated 19 genomic island regions. Among the four replicons, pAK4 was identified as essential and integral part of the genome, as supported by codon usage, GC content (66%) and synteny analysis. Comparative genome analysis for methylotrophy showed mechanistic variations in oxidation and assimilation of C1 compounds among closely related Paracoccus spp. Collectively, present study reports the functional characterization and genomic architecture of strain AK26 and provides genetic basis for quinone and isoprenoid based secondary metabolites synthesis using strain AK26.

The role of a newly isolated strain Corynebacterium pollutisoli SPH6 in waste activated sludge alkaline fermentation

Alkaline fermentation has been considered as one of the efficient methods for waste activated sludge (WAS) treatment, but usually limited by microbial fermentation activities under extreme pH condition. One newly isolated alkali-tolerant strain Corynebacterium pollutisoli SPH6 was used to assess its potential role and effect on WAS alkaline fermentation process. Results from response surface method showed that the optimal organic nitrogen degradation rate by SPH6 was obtained under temperature of 35 °C, initial pH of 10, shaking speed of 80 rpm, inoculation ratio of 6.5%. Batch-scale experiments demonstrated that, compared with the control group, the inoculation of SPH6 finally achieved higher productions with 13.4% of carbohydrates, 27.1% of protein and 25.4% of total volatile fatty acids (VFAs), and more predominant functional bacteria characterized by high-throughput sequencing, such as genera Acinetobacter in phylum Proteobacteria, Tissierella and Acetoanaerobium in phylum Firmicutes. The strain SPH6 might play a vital role in maintaining and facilitating the growth and diversity of functional bacteria in WAS alkaline fermentation process. It has implied promising practical application of the present strain in enhancing WAS reduction and utilization.

Effects of storage temperature on CH4 emissions from cattle manure and subsequent biogas production potential

CH₄ is one of the main greenhouse gases (GHGs) generated from agricultural sector, and a significant amount of it is emitted during the storage of livestock manure. To mitigate the CH₄ emissions, strong acid addition to the manure was attempted, which is only applicable to slurry-type manure. On the other hand, lowering the storage temperature could be an effective method to reduce the CH₄ emissions, particularly applicable to solid-type manure. In this study, cattle manure (CM) with a high-solid content (TS > 30%) was stored at different temperatures (15-35 °C) for 80 d. The highest CH₄ emissions of 375.1 kg CO₂ eq./ton VS was observed at 35 °C, and this was reduced to less than half at ≤20 °C. Like the difference in CH₄ emissions, the degradation of organic matter showed a similar trend. The maximum VS reduction of 29% was observed at 35 °C, while only 8% reduction was observed at 15 °C. Results from microbial community analyses and specific methanogenic activity tests indicated that hydrogenotrophic methanogens were the dominant indigenous CH₄-producers, and the abundance of psychrophilic methanogens increased with decreasing temperature. The conservation of organic matter at low temperature led to an increase in biogas production potential from 25 to 43 L CH₄/kg CM. It was calculated that the GHGs emissions from electricity consumption for cooling CM below 25 °C can be offset by mitigating CH₄ emissions during storage but increasing in subsequent biogas production potential of CM. Compared at 35 °C, 91.6 kg CO₂ eq./ton CM of GHGs reduction can be attained at 15 °C.

Corynebacterium alimapuense sp. nov., an obligate marine actinomycete isolated from sediment of Valparaíso bay, Chile

A novel Gram-positive, non-motile, non-spore-forming and aerobic bacterium, designated strain VA37-3^T, was isolated from a marine sediment sample collected at 19.2 m water depth from Valparaíso bay, Chile. Strain VA37-3^T exhibits 97.6 % 16S rRNA gene sequence similarity to Corynebacterium marinum D7015^T, 96.4 % to Corynebacterium humireducens MFC-5^T and 96 % to Corynebacterium testudinoris M935/96/4^T; and a rpoB gene sequence similarity of 85.1 % to Corynebacterium pollutisoli VMS11^T, both analyses suggesting that strain VA37-3^T represents a novel species of Corynebacterium. Physiological testing indicated that strain VA37-3^T requires artificial sea water or sodium-supplemented media for growth, representing the first obligate marine actinomycete of the genus Corynebacterium. The genome of the proposed new species, along with the type strains of its most closely related species were sequenced and characterized. In silico genome-based similarity analyses revealed an ANIb of 72.8 % (C. marinum D7015^T), ANIm of 85.0 % (Corynebacterium mustelae DSM 45274^T), tetra of 0.90 (Corynebacterium callunae DSM 20147^T) and ggdc of 24.7 % (Corynebacterium kutscheri DSM 20755^T) when compared with the closest related strains. The genomic DNA G+C content of strain VA37-3^T was 57.0 %. Chemotaxonomic assessment of strain VN6-2^T showed the major fatty acids were C18 : 1ω9c and C16 : 0. Menaquinones predominantly consisted of MK-8(II-H2). Polar lipids consisted of diphosphatidylglycerol, glycolipids, phosphatidylglycerol, phosphoglycolipid and phosphatidylinositol. Mycolic acids also were present. Overall, the results from phylogenetic, phenotypic and genomic analyses confirmed that strain VA37-3^T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium alimapuense sp. nov. is proposed, with VA37-3^T as the type strain (=CCUG 69366^T=NCIMB 15118^T).

Application of a novel strain Corynebacterium pollutisoli SPH6 to improve nitrogen removal in an anaerobic/aerobic-moving bed biofilm reactor (A/O-MBBR)

A novel bacterium Corynebacterium pollutisoli SPH6 was added in A/O-MBBR system to explore its potential in nitrogen removal. Sodium acetate was found to be its favorable carbon sources compared to glucose, sucrose and methanol. Response surface methodology analysis revealed that SPH6 has the maximum specific degradation rate of total nitrogen (4.9302 mg N/(mg·cells·h^-1)) with the temperature of 30.5 °C, pH of 7.97, inoculation ratio of 7.73% and the ratio of chemical oxygen demand and total nitrogen (COD/TN) of 7.77. The inoculation of SPH6 in A/O-MBBR demonstrated that the strain SPH6 could substantially improve the TN removal efficiency with 20% averagely. The results of high-throughput sequencing showed that the inoculation of SPH6 would essentially improve the microbial community involving nitrogen removal genus such as Hydrogenophaga, Desulfuromonas, and Desulfomicrobium. This study is of importance in providing microbial sources for bioaugmentation in nitrogen removal of wastewater treatment.

Corynebacterium fournierii sp. nov., isolated from the female genital tract of a patient with bacterial vaginosis

Strain Marseille-P2948^T, a novel Gram-positive, catalase-positive bacterium was isolated from a vaginal sample of a patient with bacterial vaginosis. It was characterised using the taxonogenomic approach. Phylogenetic analysis revealed that the 16S rRNA and the rpoB genes exhibit 98.7 and 93.4% similarity, respectively, with those of Corynebacterium ureicelerivorans strain IMMIB RIV-301^T. Biochemical tests of strain Marseille-P2948^T gave results that were similar to those of other validly named Corynebacterium species, whereas chemotaxonomic tests showed the presence of C_16:0, C_18:1n9, C_18:0, and C_18:2n6 in the fatty acid profile. The draft genome of strain Marseille-P2948^T is 2,383,644 bp long in size with a G+C content of 65.03%. Of the 2210 predicted genes, 2147 are protein-coding genes and 63 are RNAs. Based on phenotypic, phylogenic and genomic results, it was concluded that the isolate represents a new species within the genus Corynebacterium. The name Corynebacterium fournierii sp. nov. is proposed and the type strain is Marseille-P2948^T (= CSUR P2948 = DSM 103271).

Corynebacterium defluvii sp. nov., isolated from Sewage

A Gram-positive, aerobic, non-motile, rod-shapeds, catalase-positive, and oxidase-negative strain, designated Y49^T, was isolated from sewage collected from Jilin Agricultural University, China. It grew at 20-40°C (optimum at 30°C), at pH 6.0-8.0 (optimum at 7.0) and at 0-1.0% sodium chloride (optimum at 0%). The major isoprenoid quinone was menaquinone-8 (MK-8) and the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, four unidentified lipids, and two unidentified aminolipids. The peptidoglycan was meso-diaminopimelic acid. The cell-wall sugars were galactose, arabinose, and glucose. The fatty acids were C_9:0, C_16:0, C_16:1 ω9c, C_17:1 ω9c, C_18:3 ω6c (6,9,12), C_18:1 ω9c, and C_18:0. The DNA G+C content was 51.4 mol%. Based on the 16S rRNA gene sequence analysis, the nearest phylogenetic neighbors of strain Y49^T were Corynebacterium efficiens DSM 44549^T (97.5%), Corynebacterium callunae DSM 20147^T (97.2%), Corynebacterium deserti GIMN 1.010^T (96.8%), Corynebacterium glutamicum ATCC 13032^T (96.4%), and other species belonging to this genus (92.3-95.4%). The DNA-DNA relatedness value between strain Y49^T and C. efficiens DSM 44549^T, C. callunae DSM 20147^T, C. deserti GIMN1.010^T, and C. glutamicum ATCC 13032^T was 25.5±2.0%, 21.1±1.0%, 16.5±0.5%, and 13.5±0.9%, respectively. Based on the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain Y49^T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium defluvii sp nov. is proposed. The type strain is Y49^T (= KCTC 39731^T =CGMCC 1.15506^T).