Search

Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066 T and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066 T carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066 T might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter"., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes., Competing Interests: Conflict of Interest The authors declare no competing interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Objective: The family Paenibacillaceae is linked to the order Caryophanales. Paenibacillaceae members residing in compost or soil play crucial roles in nutrient recycling and breaking down complex organic materials. However, our understanding of Paenibacillaceae remains limited., Methods: Strain SYSU GA230002 T was conclusively identified using a polyphasic taxonomic approach frequently utilized in bacterial systematics. Standard microbiological techniques were employed to characterize the morphology and biochemistry of strain SYSU GA230002 T ., Results: An anaerobic and gram--negative bacterium, designated SYSU GA230002 T , was isolated from geothermally heated soil of Tengchong, Yunnan Province, south-west China. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain SYSU GA230002 T belongs to the family Paenibacillaceae. 16S rRNA gene sequence similarity (<94.0 %), ANI (<71.95 %) and AAI values (<58.67 %) between strain SYSU GA230002 T with other members of the family were lower than the threshold values recommended for distinguishing novel species. Growth was observed at 30-45 °C (optimum, 37 °C), pH 7.0-8.0 (optimum, pH 7.5) and in 0-3.0 % (w/v) NaCl concentrations (optimum, 0 %). The major fatty acids detected were anteiso-C 15:0 , iso-C 16:0 and iso-C 17:0 . The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminolipid and two unidentified glycolipids. The respiratory quinone was MK-7. The DNA G + C content of strain SYSU GA230002 T was 49.87 %., Conclusion: Based on the results of morphological, physiological properties, and chemotaxonomic characteristics, this strain is proposed to represent a new species of a new genus Ferviditalea candida gen. nov., sp. nov. The type strain of the type species is SYSU GA230002 T (=KCTC 25726 T  = GDMCC 1.4160 T )., Competing Interests: Declaration of competing interest The authors declare that there are no conflicts of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes (MAGs) from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade., (© The Author(s) [2024]. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

A novel actinomycete, designated strain q2 T , was isolated from the saline-alkaline soil, collected from Daqing, Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain q2 T belongs to the genus Isoptericola, and showed the highest sequence similarity to Isoptericola halotolerans KCTC 19046 T (98.48%) and Isoptericola chiayiensis KCTC 19740 T (98.13%), respectively. The average nucleotide identity values between strain q2 T and other members of the genus Isoptericola were lower than 95% recommended for distinguishing novel prokaryotic species. Cells of strain q2 T were Gram-staining-positive, aerobic, non-motile, rod-shaped and non-spore-forming. Colonies of strain q2 T were golden-yellow pigmented, tidy edged and smooth surfaced. Growth occurred at 15-37 °C (optimum, 29 °C), pH 7.0-10.0 (optimum, pH 8.0). The predominant respiratory quinones were MK-9(H 4 ) and MK-9(H 2 ). The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside. The peptidoglycan compositions were L-alanine, D-aspartic, L-glutamic acid and L-lysine (type A4α). The major cellular fatty acids (> 10%) were anteiso-C 15:0 , iso-C 15:0 , and anteiso-C 17:0 . The G+C content of the genomic DNA was determined to be 69.7%. Based on the phenotypic, physiological, genotypic, and phylogenetic data, strain q2 T represents a novel species of the genus Isoptericola, for which the name Isoptericola croceus sp. nov. is proposed. The type strain is q2 T (= GDMCC 1.2923 T  = KCTC 49759 T )., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

An isolate, designated CFH 74404 T , was recovered from a hot spring in Tengchong, Yunnan province, PR China. Phylogenetic analysis indicated that the isolate belongs to the family Thermomicrobiaceae and showed the highest 16S rRNA gene sequence similarity to Thermorudis peleae KI4 T (93.6 %), Thermorudis pharmacophila WKT50.2 T (93.1 %), Thermomicrobium roseum DSM 5159 T (92.0 %) and Thermomicrobium carboxidum KI3 T (91.7 %). The average amino acid identity and average nucleotide identity values between strain CFH 74404 T and the closest relatives were 42.0-75.9 % and 67.0-77.3 %, respectively. Cells of strain CFH 74404 T stained Gram-positive and were aerobic, non-motile and short rod-shaped. Growth occurred at 20-65 °C (optimum, 55 °C), pH 6.0-8.0 (optimum, pH 7.0) and with up to 2.0 % (w/v) NaCl (optimum 0-1.0 %, w/v). The predominant respiratory quinone was MK-8. The major fatty acids (>10 %) were C 18 : 0 (50.8 %) and C 20 : 0 (16.8 %). The polar lipid profile of strain CFH 74404 T included diphosphatidylglycerol, four unidentified phosphoglycolipids, phosphatidylinositol and three unidentified glycolipids. The G+C content of the genomic DNA was determined to be 67.1 mol% based on the draft genome sequence. On the basis of phenotypic, phylogenetic and genotypic analyses, it is concluded that strain CFH 74404 T represents a new species of a novel genus Thermalbibacter of the family Thermomicrobiaceae , for which the name Thermalbibacter longus gen. nov., sp. nov. is proposed. The type strain is CFH 74404 T (=KCTC 62930 T =CGMCC 1.61585 T ).

A novel anaerobic bacterium, designated SYSU GA19001 T , was isolated from a hot spring sediment sample. Phylogenetic analysis indicated that the isolate belongs to the genus Clostridium , and showed the highest sequence similarity to Clostridium swellfunianum CICC 10730 T (96.63 %) and Clostridium prolinivorans PYR-10 T (96.11 %). Cells of strain SYSU GA19001 T were Gram-stain-positive, spore-forming, rod-shaped (0.6-0.8×2.6-4.0 µm) and motile. Growth was observed at pH 5.0-9.0 (optimum, pH 7.0), 37-55 °C (optimum, 45 °C) and in NaCl concentrations of 0-2.0 % (optimum, 0 %). The genomic DNA G+C content was 31.62 %. The major cellular fatty acids of strain SYSU GA19001 T were C 14 : 0 , iso-C 15 : 0 , C 16 : 0 and summed feature 8. The prominent polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol. Meso -diaminopimelic acid was the diamino acid in peptidoglycan. Based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, strain SYSU GA19001 T represents a novel species of the genus Clostridium , for which the name Clostridium caldaquaticum sp. nov. is proposed. The type strain of the proposed novel species is SYSU GA19001 T (=NBRC 115040 T = CGMCC 1.17864 T ).

Objectives: Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited., Methods: In this study, the endophytes were isolated under anaerobic condition from the roots of Paris polyphylla Smith var. yunnanensis. Subsequently, a polyphasic taxonomic approach was used to clarify their taxonomic positions. The fermentation products were measured in the isolates with HPLC analysis. Comparative genomics was performed on these new strains and other relatives., Results: In total, nine endophytic strains belonging to the genus Clostridium sensu stricto were isolated, and three of them were identified as new species. Seven of nine strains could produce acetate, propionate, and butyrate. Only two strains could produce ethanol, although genomics analysis suggested that only two of them were without genes for solventogenesis. Different from the endophytic strains, the phylogenetically closely related non-endophytic strains showed significant enrichment effects on some metabolic pathways involving environmental information processing, carbohydrate, and amino acid metabolisms, etc. It suggests that the genomes of these endophytic strains had undergone subtle changes associated with environmental adaptations., Conclusion: Consequently, strains YIM B02505 T , YIM B02515 T , and YIM B02565 T are proposed to represent a new species of the genus Clostridium sensu stricto, for which the names Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov. are suggested., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Microbes are widespread in the sea that covers more than two-thirds of the earth's surface and most microorganisms living in the marine environment have yet to be cultured. Previous studies showed that drying treatment, a strategy of sample pre-treatment widely applied in microbial isolation and incubation, may alter the cultivable microbial diversity, such as Actinomycetota, essential for exploring novel secondary metabolites from the marine environment, isolated from drying-treated samples. However, whether drying treatments actually can change microbial community diversity and how the drying treatments of samples influence the cultivable microbial diversity of marine samples have not yet adequately been evaluated. Here, three marine sediment samples were dried and incubated at 28 ºC, 37 ºC, and 45 ºC, and the microbial diversity was assessed with high-throughput sequencing. Our results suggested that drying treatments had different effects on different genera and some potential novel species could be cultured only from drying-treated samples, including the novel members from the families Paenibacillaceae and Thermoactinomycetaceae. Non-metric multidimensional scaling analysis showed that the treated samples were clustered according to the cultivation temperatures rather than the drying conditions at high cultivation temperatures. However, at the cultivation temperatures of 28 ºC, drying treatments were the larger separation between cultivable microbial communities in the process of microbial isolation. These results showed that the drying treatments influenced the cultivated microbes in a taxon-specific pattern and extended potential novel taxa. Combining high-throughput sequencing to various drying conditions and incubation temperatures, this study provides new insight into the effects of drying treatment on the cultivable microbial diversity of marine sediments., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

COVID-19 has posed unprecedented challenges to global public health since its outbreak. The Qing-Fei-Pai-Du decoction (QFPDD), a Chinese herbal formula, is widely used in China to treat COVID-19. It exerts an impressive therapeutic effect by inhibiting the progression from mild to critical disease in the clinic. However, the underlying mechanisms remain obscure. Both SARS-CoV-2 and influenza viruses elicit similar pathological processes. Their severe manifestations, such as acute respiratory distress syndrome (ARDS), multiple organ failure (MOF), and viral sepsis, are correlated with the cytokine storm. During flu infection, QFPDD reduced the lung indexes and downregulated the expressions of MCP-1, TNF-[Formula: see text], IL-6, and IL-1[Formula: see text] in broncho-alveolar lavage fluid (BALF), lungs, or serum samples. The infiltration of neutrophils and inflammatory monocytes in lungs was decreased dramatically, and lung injury was ameliorated in QFPDD-treated flu mice. In addition, QFPDD also inhibited the polarization of M1 macrophages and downregulated the expressions of IL-6, TNF-[Formula: see text], MIP-2, MCP-1, and IP-10, while also upregulating the IL-10 expression. The phosphorylated TAK1, IKK[Formula: see text]/[Formula: see text], and I[Formula: see text]B[Formula: see text] and the subsequent translocation of phosphorylated p65 into the nuclei were decreased by QFPDD. These findings indicated that QFPDD reduces the intensity of the cytokine storm by inhibiting the NF-[Formula: see text]B signaling pathway during severe viral infections, thereby providing theoretical and experimental support for its clinical application in respiratory viral infections.

Biological denitrification is a significant process in nitrogen biogeochemical cycle of terrestrial geothermal environments, and Thermus species have been shown to be crucial heterotrophic denitrifier in hydrothermal system. Five Gram-stain negative, aerobic and rod-shaped thermophilic bacterial strains were isolated from hot spring sediments in Tibet, China. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences indicated that these isolates should be assigned to the genus Thermus and were most closely related to Thermus caldifontis YIM 73026 T , and Thermus brockianus YS38 T . Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the five strains and the type strains of the genus Thermus were lower than the threshold values (95% and 70%, respectively) recommended for bacterial species, which clearly distinguished the five isolates from other species of the genus Thermus and indicated that they represent independent species. Colonies are circular, convex, non-transparent. Cell growth occurred at 37-80 °C (optimum, 60-65 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-2.0% (w/v) NaCl (optimum, 0-0.5%). Denitrification genes (narG, nirK, nirS, and norB genes) detected in their genomes indicated their potential function in nitrogen metabolism. The obtained results combined with those of morphological, physiological, and chemotaxonomic characteristics, including the menaquinones, polar lipids, and cellular fatty acids showed that the isolates are proposed as representing five novel species of the genus Thermus, which are proposed as Thermus hydrothermalis sp. nov. SYSU G00291 T , Thermus neutrinimicus sp. nov. SYSU G00388 T , Thermus thalpophilus sp. nov. SYSU G00506 T , Thermus albus sp. nov. SYSU G00608 T , Thermus altitudinis sp. nov. SYSU G00630 T ., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

A novel bacterium, designated strain APA&#95;H-1(4) T , was isolated from the saline-alkaline soil, Zhaodong, Heilongjiang Province, China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus, and showed the highest sequence similarity to O. damuensis KCTC 33146 T (98.35%, similarity) and 'O. massiliensis' DSM 24644 (98.32%). The average nucleotide identity values between strain APA&#95;H-1(4) T and other members of the genus Oceanobacillus were lower than 82% recommended for distinguishing novel prokaryotic species. The digital DNA-DNA hybridization values of strain APA&#95;H-1(4) T with O. damuensis KCTC 33146 T and 'O. massiliensis' DSM 24644 were 13.60 and 17.60%, respectively. Cells of strain APA&#95;H-1(4) T were Gram-staining positive, motile, aerobic, spore-forming rods (0.5-0.7 × 1.8-2.6 μm) with flagella. The growth was found to occur optimally at 37 °C. The whole-cell hydrolysate contained meso-diaminopimelic acid as the diagnostic cell wall diamino acid. The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified polar lipid. The predominant respiratory quinone was identified as menaquinone-7 (MK-7). The major cellular fatty acid (>10%) was anteiso-C 15:0 . The G + C content of the genomic DNA was determined to be 38.4% based on the draft genome sequence. Based on the comparative analysis of polyphasic taxonomic data, strain APA&#95;H-1(4) T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus saliphilus sp. nov. is proposed. The type strain is APA&#95;H-1(4) T (=GDMCC 1.2239 T  = KCTC 43254 T )., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

A thermophilic bacterium, designated strain SYSU G04325 T , was isolated from a hot spring sediment in Yunnan, China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G04325 T shows high sequence similarity to Thermoflexibacter ruber NBRC 16677 T (86.2%). The strain can be differentiated from other species of the family Thermoflexibacteraceae by its distinct phenotypic and genotypic characteristics. Cells of the strain SYSU G04325 T were observed to be aerobic, Gram-stain negative and filamentous. Growth was found to occur optimally at 45 ºC and pH 7.0. In addition, the respiratory quinone was identified as menaquinone-7, while the major fatty acids (> 10%) were identified as iso-C 15:0 , iso-C 17:0 and Summed Feature 9 (iso-C 17:1 ω9c). The polar lipids detected included phosphatidylethanolamine, three unidentified phospholipids, one unidentified glycolipid, five unidentified aminolipids and four unidentified polar lipids. The G + C content of the genomic DNA was determined to be 47.6% based on the draft genome sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G04325 T is concluded to represent a novel species of a novel genus in the family Thermoflexibacteraceae, for which the name Rhodoflexus caldus gen. nov., sp. nov. is proposed. The type strain of Rhodoflexus caldus is SYSU G04325 T (= MCCC 1K06127 T  = KCTC 82848 T )., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

A novel Gram-stain-negative, non-motile, short rod-shaped and aerobic bacterial strain, designated as CFH 74456  T , was isolated from sediment of a hot spring, Tengchong, Yunnan Province, south-western China. Growth occurred at 20-53 ºC (optimum 45 ºC), pH 7.0-9.0 (optimum pH 8.0) and up to 2.0% (w/v) NaCl (optimum 0-1.0%, w/v). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids (> 10%) were C 17:1 ω6c (17.9%) and summed feature 8 (38.6%). The polar lipid profile of strain CFH 74456  T was identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, three unidentified glycolipids and three unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CFH 74456  T belongs to the genus Qipengyuania, and was most closely related to Qipengyuania sediminis CGMCC 1.12928  T (95.7%). The draft genome size of the isolate was 2.29 Mb with G + C content of 68.5%. The amino acid identity, average nucleotide identity and the digital DNA-DNA hybridization values between strain CFH 74456  T and the closest relatives ranged from 67.0 to 67.9%, 73.0 to 74.2% and 18.2-19.3%, respectively. On the basis of phenotypic, phylogenetic and genotypic analyses, it is concluded that strain CFH 74456  T represents a new species of the genus Qipengyuania, for which the name Qipengyuania thermophila sp. nov. is proposed. The type strain is CFH 74456  T (= KCTC 62921  T  = CCTCC AB 2018237  T )., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Phylogenomic analyses were performed on the nine species of the genus Meiothermus and four species of the genus Calidithermus. Phylogenetic analysis, low values of genomic relatedness indices and functional diversity analysis indicated that Meiothermus silvanus should not be classified within the clades for Meiothermus and Calidithermus but instead be reclassified as a new genus, for which we propose the name Allomeiothermus gen. nov., with Allomeiothermus silvanus comb. nov. as type species. In addition, the species Meiothermus cateniformans Zhang et al. (Int J Syst Evol Microbial 60:840-844, 2010) should also be reclassified as a later heterotypic synonym of Meiothermus taiwanensis Chen et al. (Int J Syst Evol Microbiol 52:1647-1654, 2002) emend. Raposo et al. (2019). This reclassification is based on the high genomic relatedness indices (98.8% ANI; 90.2% dDDH; 99% AAI) that are above the threshold values necessary for defining a new species, as well as on the observation of overlapping functions on Principal Coordinate Analysis plot generated from Clusters of Orthologous Genes., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to " Candidatus Brocadia," " Candidatus Kuenenia," " Candidatus Scalindua," " Candidatus Anammoxoglobus," and " Candidatus Jettenia" were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 10 4 to 1.20 × 10 7 copies L -1 . Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Liu, Lv, Narsing Rao, Ming, Salam, Li, Liu, Zhang, Zhang, Xian, Jiao and Li.)

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H 2 -dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism., (© 2021. The Author(s), under exclusive licence to International Society for Microbial Ecology.)

Two bacterial strains SYSU G02173 T and SYSU G03142 were isolated from hot springs in Tibet, China. Based on the results of nearly full-length 16S rRNA gene sequences and phylogenetic analyses, strains SYSU G02173 T and SYSU G03142 were assigned to the family Sphingosinicellaceae, and were closest to Sandaracinobacter sibiricus RB16-17  T (96.04% and 96.12% similarity, respectively). Cells of the both new strains were observed to be motile rod-shape, Gram-staining negative. Growth occurred at pH 6-8 (optimal: pH 7.0) and 37-55 °C (optimal: 45 °C) with 0-1.0% (w/v) NaCl in T4 broth. The cells were found to be positive for oxidase and catalase activities. The major respiratory ubiquinone was Q-8. The major fatty acids were identified as summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c), C 16:0 , C 14:0 2-OH. The major polar lipids were found to consist of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, one unidentified glycolipid, three unidentified aminolipids and two unidentified polar lipids. The DNA G + C contents of strains SYSU G02173 T and SYSU G03142 were 71.8%. The average nucleotide identity (ANI) value between strain SYSU G02173 T and SYSU G03142 was 99.98%. The amino acid identity (AAI) values between them and their closely related species were below 66.14%. The isolates are characterized by aerobic growth, a yellow endocellular pigment and a higher optimum growth temperature. The results showed that strains SYSU G02173 T and SYSU G03142 represent a novel species of a novel genus in the family Sphingomonadaceae, and thus the name Thermaurantiacus tibetensis (type strain SYSU G02173 T  = KCTC 72052  T  = CGMCC 1.16680  T ) is proposed.

Two anaerobic bacteria, designated strains SYSU GA16112 T and SYSU GA16107, were isolated from a hot spring in Tengchong County, Yunnan Province, south-west PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SYSU GA16112 T and SYSU GA16107 belong to the family Dysgonamonadaceae . Cells of strains SYSU GA16112 T and SYSU GA16107 were Gram-stain-negative, rod-shaped and non-motile. The major fatty acids (>10 %) of strains SYSU GA16112 T and SYSU GA16107 were identified as anteiso-C 15 : 0 and anteiso-C 17 : 0 3OH. The polar lipid profile of strain SYSU GA16112 T was found to consist of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phosphoglycolipids, two unidentified aminolipids and one unidentified polar lipid, while that of strain SYSU GA16107 consisted of phosphatidylethanolamine, two unidentified polar lipids, three unidentified aminophospholipids, two unidentified phosphoglycolipids and one unidentified aminolipid. The genomic DNA G+C contents of strains SYSU GA16112 T and SYSU GA16107 were determined to be 41.90 and 41.89 %, respectively, and the average nucleotide identity value between them was 99.99 %. Based on their morphological and physiological properties, and results of phylogenetic analyses, strains SYSU GA16112 T and SYSU GA16107 are considered to represent a novel species of a novel genus, for which the name Seramator thermalis gen. nov., sp. nov. (type strain SYSU GA16112 T =CGMCC 1.5281 T =KCTC 15753 T ) is proposed.

Lignocellulose is considered a major source of renewable energy that serve as an alternative to the fossil fuels. Members of the genus Clostridium are some of the many microorganisms that have the ability to degrade lignocellulose efficiently to sugar, which can be further converted to biofuel. In this study, we isolated twelve Clostridium strains from hot spring samples of Yunnan and Tibet, of which isolates SYSU GA15002 T and SYSU GA17076 showed low 16S rRNA gene sequence identity profiles to any of the validly named Clostridium strains (<94.0%). Studies using a polyphasic taxonomy approach concluded that the two isolates represent one novel species of the genus Clostridium, for which we propose the name Clostridium thermarum sp. nov., with SYSU GA15002 T as the type strain of the species. Isolate SYSU GA15002 T has an optimum growth temperature at 45°C. Fermentation of the substrates cellobiose, cellulose, xylan and untreated straw powder by this strain results in the production of ethanol, along with acetate and formate. The complete pathways for the conversion of cellulose and xylan to ethanol is also predicted from the genome of isolate SYSU GA15002 T , which revealed a single step conversion of lignocellulosic biomass through consolidated bioprocessing. This paper is a comprehensive study encompassing isolation, polyphasic taxonomy, lignocellulose biodegradation and the genomic information of Clostridium in Yunnan-Tibet hot springs., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

In our search for novel anaerobes with potential carbohydrate polymers degrading activity, we have isolated a xylan-degrading bacterial strain SYSU GA17129 T from an anammox bacteria dominant wastewater treatment plant. Phylogenetic analysis of the 16S rRNA gene sequence indicated the strain SYSU GA17129 T belong to the order Clostridiales and shared highest sequence identity with Caldicoprobacter faecalis DSM 20678 T (89.9%). The strain was thermophilic, obligately anaerobic, non-motile and rod shaped. Optimum growth of the strain was observed at 45 °C, pH 8.0 and in the presence of 0.5% NaCl (w/v). The chemotaxonomic features of the strain SYSU GA17129 T comprised of C 14:0 FAME, iso-C 15:0 FAME and C 16:0 FAME as the major fatty acids (>10%), diphosphatidylglycerol, phosphatidylinositol mannoside, an unidentified phospholipid, three unidentified polar lipids and two unidentified glycolipids as its polar lipids, and meso-diaminopimelic acid (meso-DAP) as the diamino acid in peptidoglycan. The G + C content of the genomic DNA was 35.9%. The strain could be distinguished from other defined families within the order Clostridiales by the differences in phenotypic and physiological characteristics, distinct phylogenetic lineage in 16S rRNA gene- and genome-based phylogenies and low genomic relatedness index. Based on these distinguishing properties, strain SYSU GA17129 T is proposed to represent a new species of a new genus Xylanivirga thermophila gen. nov., sp. nov., within a new family Xylanivirgaceae fam. nov. The type species of the new taxon is SYSU GA17129 T (=KCTC 15754 T  = CGMCC 1.5282 T ). This strain is characterized within the order Clostridiales, class Clostridia of the phylum Firmicutes., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

One thermophilic bacterium, designated strain SYSU G02662 T , was isolated from hot spring sediment sampled in Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G02662 T showed the highest sequence similarity to Actinomarinicola tropica SCSIO 58843 T (95.1 %). The strain could be differentiated from other species of the family Iamiaceae by its distinct phenotypic and genotypic characteristics. Cells of strain SYSU G02662 T were aerobic, Gram-staining-positive and short rodshaped. Growth occurred optimally at 45 °C and pH 7.0. In addition, meso -diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The respiratory quinone was MK-9 (H 8 ), while the major fatty acids (>10 %) were C 16 : 0 , C 17 : 0 , C 18 : 0 and iso-C 16 : 0 . The detected polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The G+C content of the genomic DNA was 70.5 % based on the draft genomic sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G02662 T represents a novel species of a novel genus in the family Iamiaceae , for which the name Rhabdothermincola sediminis gen. nov., sp. nov. is proposed. The type strain of the proposed novel species is SYSU G02662 T (=CGMCC 4.7688 T =KCTC 49500 T ).

Clinical application evaluation research of Guidelines for the Diagnosis and Treatment of Common Diseases of Pediatrics in Traditional Chinese Medicine intends to evaluate the quality level and clinical application of the guideline. A questionnaire and prospective case survey methods were used to evaluate the applicability evaluation based on the clinician questionnaire and the application evaluation based on clinical case observation. The applicability evaluation, familiarity and utilization rate of doctors' guidelines were 85.06%, 62.76%; Sort by technical grade, intermediate grade doctors have a higher familiarity rate and utilization rate, while the junior grade doctor's is lower; Guide quality level of applicability evaluation, other items' rational percentage are better than 96% except the items of health preserving and prevention and other treatment is relatively low; Items' applicable percentage of applicability evaluation are more than 91% except the item of guide simplicity. Comprehensive applicability evaluation, The percentage of the guideline applicable to clinical practice accounted for 94.94%. The consistency rate of syndrome differentiation and clinical application is more than 96% in addition to prescription medication, other treatments and health preserving and prevention of the guidelines apply consistency of application evaluation. The percentage of good treatment effect accounted for 92.96% of application effect evaluation. The safety percentage is 99.89% and economy is 97.45%. The research shows that of Guidelines for the Diagnosis and Treatment of Common Diseases of Pediatrics in Traditional Chinese Medicine quality level is good and is basically applicable to pediatric clinical practice which can be used as a standardized recommendation of pediatric common diseases' treatment specification. A small part of the guidelines are not applicable and need to be further consummated. Health preserving and prevention and other treatment of the guideline need to be revised., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Chinese Pharmaceutical Association.)

Being exposed to specific syndromes of Chinese medicine (CM) and being compatible with other Chinese herbs are two necessary methods for controlling the toxicity of toxic Chinese herbs. The complexity of Chinese herbal components causes the difficulties in in-depth study of toxicity control. Under the guidance of systems biology, authors studied protein expression profiles and metabolite spec- trums by Chinese herbal compatible components intervening animal model with specific syndrome of CM, thus clarifying corresponding biomarkers relevant to toxicity reducing and control. Authors found out key molecules and pathways for toxicity reducing and control by molecular network technologies using and o- verlaying information integrating. All these mentioned above were finally verified by molecular biologic methods, therefore, revealing the molecular mechanism of toxicity control effects of Chinese herbal compatible components in specific syndromes of CM.

To explore the pharmacological mechanism of glycyrrhizin with series methods of systems pharmacology, main diseases related to glycyrrhizin were obtained by text mining tool; and the target proteins of glycyrrhizin were obtained via the database of Polysearch and PubChem. Then, the target proteins interaction network of glycyrrhizin was built using the software called Cytoscape. Next, the protein groups related to glycyrrhizin were analyzed by using Gene Ontology (GO) tool, and the action pathway of its target proteins was analyzed by using enrichment method. Text mining results showed that the related diseases of glycyrrhizin included chronic hepatitis C, chronic hepatitis, hepatitis, HIV virus, liver cancer and so on. Gene ontology analysis indicated that glycyrrhizin played a role mainly through modification of proteins and chromatin. The signaling pathway enrichment results showed that the main action proteins of glycyrrhizin were related to MAPK signaling pathway, toll-like receptor signaling pathway, neurotrophic factor signaling pathway, cancer and apoptosis pathways. So we can conclude that glycyrrhizin may exert its biological functions primarily by regulating multiple pathways such as MAPK signaling pathway and Toll-like receptors signaling pathway. The pharmacological action of a drug can be rapidly and comprehensively analyzed by the ways of systems pharmacology., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Chinese Pharmaceutical Association.)

As the core of traditional Chinese medicine theory, Zheng (syndrome, or pattern) classification will promote personalized medicine by changing the clinical diagnosis into a more precise mode when integrating Zheng classification with disease diagnosis approaches. The author adopted rheumatoid arthritis (RA) as a disease model, to explore the scientific fundamentals of Zheng classification based on disease diagnosis using systemic biological approaches and evidence-based medicine design, as well as developed novel approaches on the methodology of clinical effectiveness evaluation on Chinese medicine and R&D of combinational drugs design based on Fu Fang (Chinese herbal formula). Some unique research design and methods are herein introduced.

The present study aimed to explore the holistic mechanism for the antihypertrophic effect of a compound in Chinese medicine, QiShenYiQi Pills (QSYQ) and the contributions of its components to the effect in rats with cardiac hypertrophy (CH). After induction of CH by ascending aortic stenosis, rats were treated with QSYQ, each identified active ingredient (astragaloside IV, 3, 4-dihydroxy-phenyl lactic acid or notoginsenoside R1) from its 3 major herb components or dalbergia odorifera, either alone or combinations, for 1 month. QSYQ markedly attenuated CH, as evidenced by echocardiography, morphology and biochemistry. Proteomic analysis and western blot showed that the majority of differentially expressed proteins in the heart of QSYQ-treated rats were associated with energy metabolism or oxidative stress. Each ingredient alone or their combinations exhibited similar effects as QSYQ but to a lesser extent and differently with astragaloside IV and notoginsenoside R1 being more effective for enhancing energy metabolism, 3, 4-dihydroxy-phenyl lactic acid more effective for counteracting oxidative stress while dalbergia odorifera having little effect on the variables evaluated. In conclusion, QSYQ exerts a more potent antihypertrophic effect than any of its ingredients or their combinations, due to the interaction of its active components through a multi-component and multi-target mode.

The property theory of Chinese herbal medicine (CHM) is regarded as the core and basic of Chinese medical theory, however, the underlying mechanism of the properties in CHMs remains unclear, which impedes a barrier for the modernization of Chinese herbal medicine. The properties of CHM are often categorized into cold and heat according to the theory of Chinese medicine, which are essential to guide the clinical application of CHMs. There is an urgent demand to build a cold/heat property classification model to facilitate the property theory of Chinese herbal medicine, as well as to clarify the controversial properties of some herbs. Based on previous studies on the cold/heat properties of CHM, in this paper, we described a novel strategy on building a cold/heat property classification model based on herbal bio-effect. The interdisciplinary cooperation of systems biology, pharmacological network, and pattern recognition technique might lighten the study on cold/heat property theory, provide a scientific model for determination the cold/heat property of herbal medicines, and a new strategy for expanding the Chinese herbal medicine resources as well.

Traditional Chinese medicine (TCM) formulas with fixed combinations rely on "sovereign, minister, assistant and guide" and fuzzy mathematical quantitative law, leading to greater challenges for the identification of active ingredients. Transformation and metabolic studies involving the Phase I drug-metabolizing enzyme cytochrome P450 (CYP) might potentially solve some of these challenges. The pharmacological effects can not be attributed to one active ingredient in TCMs, but integrated effects resulting from the combined actions of multiple ingredients. However, it is only after long-term administration that most ingredients exert their actions, which can result in prolonged exposure to herbs in vivo. Therefore, interactions between herbal compounds and CYPs appear to be inevitable. Yet unlike Western drugs, experimental determination of the absorption and disposition properties is not commonly carried out for TCMs. Moreover, the use of TCM as injections is an innovation aimed to improve efficiency in extensive clinical use in Mainland China. Therefore, in recent years, cases of adverse drug reactions (ADR) mainly concerning allergic reactions involving TCMs such as ShenMai injection and QingKaiLing injection have been reported, which have attracted attention with regard to the legal responsibilities for TCM approval. The lack of information on the ADME characteristics, especially the metabolic stability and interaction potential between CYPs and herbs, increases ADR occurrence due to TCMs. In this article, we review the most common herbs used in TCM prescriptions and fixed combinations of their usable frequency, and summarize the current understanding of the ability of phytochemical ingredients to act as substrates, inhibitors or inducers of human CYP enzymes, through which the key role of CYP enzymes on the herb disposition and toxicity is highlighted. The potential interaction between herbal phytochemicals and CYP enzymes dominates the target exposure, which further helps to elucidate the herbal pharmacological basis, assess the individual toxic risk of herbal remedies and gain mechanistic insight into herb-drug interactions (HDIs).

Objective: H1N1 was a new and potentially serious infectious disease, in human, the severity of influenza can vary from mild to severe, thus to find an effective and safety way to control the influenza pandemic is of crucial importance. This retrospective study describes the duration of viral shedding in H1N1 patients that were hospitalized and treated in China., Methods: Clinical data were collected from May to July, 2009 in China for 963 patients with influenza A (H1N1) virus infection. Patients were treated based on the guidelines issued by the Chinese Ministry of Health. The primary outcome was duration of viral shedding and statistical comparisons were performed., Results: In the patients with body temperature greater than 38.0 degrees C, there were no differences in virus shedding duration among the patients taking oseltamivir within two days, patients undergoing Traditional Chinese Medicine (TCM) therapy or those receiving no drug therapy. In patients with body temperature > or =38.1 degrees C, TCM therapy reduced the viral shedding duration (P < 0.05, vs. oseltamivir therapy). Furthermore, taking oseltamivir two days after onset of symptoms might prolong the virus shedding duration (P < 0.05, vs. taking oseltamivir less than 2 days of onset)., Conclusion: TCM therapy is effective for reducing the length of virus shedding in patients with body temperature > or =38.0 degrees C. Oseltamivir used for reducing virus shedding duration should be taken within two days of onset.

Objective: To assess the quality of the first batch of Chinese evidence-based clinical practice guidelines (CPGs) in Traditional Chinese Medicine (TCM) using the Appraisal of Guidelines for Research and Evaluation (AGREE) instrument., Methods: Evidence-based CPGs in TCM supported by the World Health Organization Western Pacific Regional Office (WHO/WPRO) and whose development was organized by the China Academy of Chinese Medical Sciences were identified and manually retrieved. CPGs were assessed using the AGREE instrument, and the data in each CPG were analyzed in terms of the six domains in the AGREE instrument: scope and purpose, stakeholder involvement, rigor of development, clarity and presentation, applicability, and editorial independence., Results: Twenty-eight CPGs were identified, of which 26 were included in the study. The AGREE instrument rated the 26 CPGs in terms of the six domains. The assessment results showed the following average scores: for editorial independence, 84.16%; for rigor of development, 80.95%; for scope and purpose, 79.96%; for clarity and presentation, 70.88%; for stakeholder involvement, 61.28%; for applicability, the average score was only 27.09%. In summary, nine CPGs were rated as "strongly recommended", six as "recommended with provision or alternation", and 11 as "unsure"., Conclusion: Most of the first batch of Chinese evidence-based CPGs in TCM had significant shortcomings in applicability. It is suggested that special attention be paid to enhancing the quality of applicability when developing evidence-based CPGs in TCM.

Objective: To explore the effects of Huoxiang Zhengqi liquid (HXZQ) on enteric mucosal immune responses in mice with Bacillus dysenteriae and Salmonella typhimurium induced diarrhea (BSD)., Method: Mice were randomly divided into four groups with 10 mice in each group: control group (control), BSD group, Huoxiang Zhengqi liquid treated BSD groups at high dosage and low dosage (HXZQ high, HXZQ low). HXZQ was administrated from the day of diarrhea induction at dosage of 5.21 g kg(-1) and 0.52 g kg (-1) respectively. Peyer's patch and periphery lymphocytes were prepared for flow cytometry, and level of TNF-alpha in periphery and enteric tissue homogenate were determined with ELISA. Student's t-test was used for statistics., Result: Mice in BSD group started showing continuous diarrhea at the day of induction till the fourth day when the mice were sacrificed. Diarrhea in the mice of HXZQ high and low groups lasted for 36 and 54 h respectively. There were more CD4+ and CD8+ cells in periphery, less CD4+ cells in peyer's patch in BSD mice comparing to normal mice. In peyer's patch, there were more CD8+ cells in mice in HXZQ high and low groups and more CD4+ in mice in HXZQ high group. Higher level TNF-alpha in periphery and intestinal tissue homogenate in BSD group were observed. Mice in HXZQ high group showed the decreased level TNF-alpha in periphery and enteric tissue homogenate., Conclusion: The immune regulation on peyer's patch CD4+ and CD8+ cells and suppression on TNF-alpha level in enteric homogenate might partially explain the effect of HXZQ on improvement of BSD.

Some clinical trials showed that the efficacy of traditional Chinese medicine was not good as the efficacy of western medicine even thoush clinical doctors have been using traditional medicine effectively. Such a result originated from improper application of western medical thoughts in routine clinical efficacy evaluation. To find differences from effective cases with non-effective cases and put the differences into the indication of next clinical trial would conform to the differentiation theory in traditional Chinese medicine. The differences, whether positively or negatively related to the efficacy, could be obtained from all information including symptom evaluation, tongue appearance, pulse feeling and biological parameters with non-linear and other statistical methods. More specific indication finding would be the key task for clinical efficacy evaluation via multiple clinical trials.