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Due to their outstanding nutritional and functional properties, the traditionally fermented dairy products (TFDP) from camel, mare, and cow gained universal praise during their long history of production. In this study, the physicochemical composition and microbial communities of Khoormog, Chigee, and Airag, the TFDP from Xilin Gol in China, were investigated and compared. The physicochemical analysis revealed a higher content of total solid content, protein, and fat in Khoormog (12.5 ± 1.6%; 4.6 ± 0.7%; 4.4 ± 1.3%) compared to Chigee (7.8 ± 1.3%; 2.1 ± 0.2%; 0.8 ± 0.2%) and Airag (8.9 ± 0.7%; 3.7 ± 0.4%; 1.4 ± 0.5%). All three types of TFDP shared 41.2% of bacterial and 25.4% of fungal OTUs, and 95.34% of bacterial and 95.52% of fungal sequence reads. The bacterial and fungal community consisted of four phyla and five genera, and three phyla and seven genera, respectively. Lastly, Lactobacillus predominated in Khoormog, Chigee, and Airag at the genus level, while the dominant fungal genera varied among the samples. In conclusion, the microbial community structures of TFDP from camel, mare, and cow were not significantly different in a definite area (Xilingol region), and Khoormog, Chigee, and Airag bred the common “core microbiota”., This study is the first to investigate the nutritional properties and microbiota of Khoormog from camel's milk using high throughput sequencing. This study provides the comparative examination of the physicochemical composition and microbial community of Khoormog, Chigee, and Airag.

Phenolic glycosides are the important bioactive molecules, and their bioavailability can be influenced by enzyme hydrolysis, such as β-glucosidases (EC3.2.1.21) and other glycosyl hydrolases (GHs). Wood rotting fungi possess a superfamily of GHs, but little attention has been paid to the GHs and their potential applications in biotransformation of phenolic glycosides. In this study, two GH3 gene family members of Trametes trogii S0301, mainly expressed in the carbon sources conversion stage were cloned, and TtBgl3 coded by T_trogii_12914 showed β-glucosidase activity toward 4-nitrophenyl β-D-glucopyranoside (pNPG). The recombinant TtBgl3 preferred an intermediately neutral optimum pH with >80% of the maximum activity at pH 5.0–7.0 and was stable at a wide range of pH (5.0–10.0). Phenolic glycosides transformation experiments showed that TtBgl3 was a dual-activity enzyme with both activities of aryl-β-D-glucosidase and β-glucuronidase, and could hydrolyze the β-glucoside/glucuronide bond of phenolic glycosides. Under optimized conditions, the recombinant TtBgl3 had much higher transformation efficiency toward the β-glucoside bond of gastrodin, esculin and daidzin than β-glucuronide bond of baicalin, with the transformation rate of 100 and 50%, respectively. Our homology modeling, molecular docking, and mutational analysis demonstrated that His85 and Lys467 in the acceptor-binding pocket of TtBgl3 were the potential active sites. The point mutation of His85 and Lys467 leads to the significantly impaired catalytic activity toward pNPG and also the weak transformation efficiency toward gastrodin. These findings provide insights for the identification of novel GH3 β-glucosidases from T. trogii and other wood-rotting fungi. Furthermore, TtBgl3 might be applied as green and efficient biological catalysts in the deglycosylation of diverse phenolics to produce bioactive glycosides for drug discovery in the future.

Manganese peroxidases (MnPs), gene family members of white-rot fungi, are necessary extracellular enzymes that degrade lignocellulose and xenobiotic aromatic pollutants. However, very little is known about the diversity and expression patterns of the MnP gene family in white-rot fungi, especially in contrast to laccases. Here, the gene and protein sequences of eight unique MnP genes of T. trogii S0301 were characterized. Based on the characteristics of gene sequence, all TtMnPs here belong to short-type hybrid MnP (type I) with an average protein length of 363 amino acids, 5–6 introns, and the presence of conserved cysteine residues. Furthermore, analysis of MnP activity showed that metal ions (Mn2+ and Cu2+) and static liquid culture significantly influenced MnP activity. A maximum MnP activity (>14.0 U/mL) toward 2,6-DMP was observed in static liquid culture after the addition of Mn2+ (1 mM) or Cu2+ (0.2 or 2 mM). Moreover, qPCR analysis showed that Mn2+ obviously upregulated the Group I MnP subfamily (T_trogii_09901, 09904, 09903, and 09906), while Cu2+ and H2O2, along with changing temperatures, mainly induced the Group II MnP subfamily (T_trogii_11984, 11971, 11985, and 11983), suggesting diverse functions of fungal MnPs in growth and development, stress response, etc. Our studies here systematically analyzed the gene structure, expression, and regulation of the TtMnP gene family in T. trogii, one of the important lignocellulose-degrading fungi, and these results extended our understanding of the diversity of the MnP gene family and helped to improve MnP production and appilications of Trametes strains and other white-rot fungi.

Phenolic glycosides are the important bioactive molecules, and their bioavailability can be influenced by enzyme hydrolysis, such as β-glucosidases (EC3.2.1.21) and other glycosyl hydrolases (GHs). Wood rotting fungi possess a superfamily of GHs, but little attention has been paid to the GHs and their potential applications in biotransformation of phenolic glycosides. In this study, two GH3 gene family members of

White-rot fungi, especially Trametes strains, are the primary source of industrial laccases in bioenergy and bioremediation. Trametes strains express members of the laccase gene family with different physicochemical properties and expression patterns. However, the literature on the expression pattern of the laccase gene family in Trametes trogii S0301 and the response mechanism to Cu(2+), a key laccase inducer, in white-rot fungal strains is scarce. In the present study, we found that Cu(2+) could induce the mRNAs and proteins of the two alternative splicing variants of heat shock transcription factor 2 (TtHSF2). Furthermore, the overexpression of alternative splicing variants TtHSF2α and TtHSF2β-I in the homokaryotic T. trogii S0301 strain showed opposite effects on the extracellular total laccase activity, with maximum laccase activities of approximately 0.6 and 3.0 U ml(−1), respectively, on day 8, which are 0.4 and 2.3 times that of the wild-type strain. Similarly, TtHSF2α and TtHSF2β-I play opposite roles in the oxidation tolerance to H(2)O(2). In addition, the direct binding of TtHSF2α to the promoter regions of the representative laccase isoenzymes (TtLac1 and TtLac13) and protein-protein interactions between TtHSF2α and TtHSF2β-I were detected. Our results demonstrate the crucial roles of TtHSF2 and its alternative splicing variants in response to Cu(2+). We believe that these findings will deepen our understanding of alternative splicing of heat shock transcription factors (HSFs) and their regulatory mechanism of the laccase gene family in white-rot fungi. IMPORTANCE The members of laccase gene family in Trametes strains are the primary source of industrial laccase and have gained widespread attention. Increasing the yield and enzymatic properties of laccase through various methods has always been a topic worthy of attention, and there is no report on the regulation of laccase expression through HSF transcription factor engineering. Here, we found that two alternative splicing variants of TtHSF2 functioned oppositely in regulating the expression of laccase genes, and copper can induce the expression of almost all members of the laccase gene family. Most importantly, our study suggested that TtHSF2 and its alternative splicing variants are vital for copper-induced production of laccases in T. trogii S0301.

Background Trametes trogii is a member of the white-rot fungi family, which has a unique ability to break down recalcitrant lignin polymers to CO2 and water, and they have enormous potential to biodegrade a wide range of toxic environmental pollutants. Because of its industrial potential, the identification of lignin-degrading enzyme systems in Trametes is an important area of research. Development and utilization of industrial value genes are suffering due to deficiency knowledge of genome available for their manipulation. Results In the present study, Homokaryotic strains of T. trogii S0301 were screened and sequencing by PacBio Sequel II platform. The final draft genome is ~ 39.88 Mb, with a contig N50 size of 2.4 Mb, this was the first genome sequencing and assembly of T. trogii species. Further analyses predicted 14,508 protein-coding genes. Results showed that T. trogii S0301 contains 602 genes encoding CAZymes, include 211 glycoside hydrolase and 117 lignin-degrading family genes, nine laccases related genes. Small subunit ribosomal RNA gene (18S rRNA) sequencing confirms its phylogenetic position. Moreover, T. trogii S0301 has the largest number of cytochromes P450 (CYPs) superfamily genes compare to other fungi. All these results are consistent with enzymatic assays and transcriptome analysis results. We also analyzed other genome characteristics in the T. trogii S0301genome. Conclusion Here, we present a nearly complete genome for T. trogii S0301, which will help elucidate the biosynthetic pathways of the lignin-degrading enzyme, advancing the discovery, characterization, and modification of novel enzymes from this genus. This genome sequence will provide a valuable reference for the investigation of lignin degradation in the Trametes genus.

Additional file 6. BUSCO validation of the T. trogii S0301 genome annotation result.

Additional file 5. Gene annotation of the T. trogii S0301 genome.

Additional file 1. Genome comparisons with other Trametes species.

Additional file 9. Repeats content of the T. trogii S0301 genome.

Using response surface methodology, the maximum laccase activity of 122.9 U ml −1 was obtained in Trametes trogii S0301. The major isoform of the laccase secreted in the optimized medium was purified by 4-fold to a specific activity of 352.1 U mg −1 protein. The laccase (a molecular mass of 56 kDa), acted optimally at pH 3.0 and exhibited an optimum temperature of 45 °C using ABTS as substrate, with the half-life at 60 °C and 75 °C for 3 h and 10 min, respectively. The purified laccase was highly resistant to Co 2+ , Cu 2+ , Zn 2+ and Mn 2+ (100 mM). In addition, the purified laccase was effective to decolorize malachite green, bromophenol blue, crystal violet and acid red without the addition of redox mediators. Peptide-mass fingerprinting analysis by MALDI-TOF MS showed the purified laccase of T. trogii S0301 was a typical laccase isoform, which shared 99.3% identity with a laccase from Coriolopsis gallica . Further, the full-length DNA of the laccase was cloned based on the highly conservative copper-binding domains using degenerate PCR and TAIL-PCR, and the deduced amino acid sequence of the matured protein matched exactly with the peptides of the purified laccase.

The phylogeny of methanogenic archaea associated with ciliate protozoa in a sheep rumen was investigated. Ruminal ciliate protozoa were exhaustively washed and mixtures of genomic DNA extracted. Archaea-specific nested PCR amplification was conducted with the ciliate genomic mixture. The resultant small subunit (16S) ribosomal RNA gene (ssu rDNA) was cloned into Escherichia coli JM 109. Many methanogens were still observed on and/or in ciliate cells by fluorescent microscopy even after exhaustive washing with buffer. Partial sequences of ssu rDNA close to Methanobrevibacter smithii were dominant in the retrieved sequences. RFLP analyses on the retrieved sequences revealed the absence of Methanobrevibacter ruminantium in the protozoal preparation. The association of Methanobrevibacter spp. with ruminal ciliate protozoa was demonstrated by the isolation of archaeal ssu rDNA phylogenetically close to that of M. smithii.

A novel thermophilic Gram staining positive strain Rx1 was isolated from hot springs in Baoshan of Yunnan Province, China. The strain was characterized as a hemicellulose-decomposing obligate anaerobe bacterium that is rod-shaped (diameter: 0.5–0.7 μm; length: 2.0–6.7 μm), spore-forming, and motile. Its growth temperature range is 38–68 °C (optimum 50–55 °C) and pH range is 4.5–8.0 (optimum 7.0). The maximum tolerance concentration of NaCl was 3 %. Rx1 converted thiosulfate to elemental sulfur and reduced sulfite to hydrogen sulfide. The bacterium grew by utilizing xylan and starch, as well as a wide range of monosaccharide and polysaccharides, including glucose and xylose. The main products of fermentation were ethanol, lactate, acetate, CO2, and H2. The maximum xylanase activity in the culture supernatant after 30 h of incubation at 55 °C was 16.2 U/ml. Rx1 DNA G + C content was 36 mol %. 16S rRNA gene sequence analysis indicated that strain Rx1 belonged to the genus Thermoanaerobacterium of the family ‘Thermoanaerobacteriaceae’ (Firmicutes), with Thermoanaerobacterium aciditolerans 761–119 (99.2 % 16S rRNA gene sequence similarity) being its closest relative. DNA–DNA hybridization between Rx1 and T. aciditolerans 761–119 showed 36 % relatedness. Based on its physiological and biochemical tests and DNA–DNA hybridization analyses, the isolate is considered to represent a novel species in the genus Thermoanaerobacterium, for which the name Thermoanaerobacterium calidifontis sp. nov. is proposed, with the type strain is Rx1 (=JCM 18270 = CCTCC M 2011109). Electronic supplementary material The online version of this article (doi:10.1007/s00203-013-0895-5) contains supplementary material, which is available to authorized users.