Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model.

Hyperuricemia (HUA) is a metabolic syndrome caused by abnormal purine metabolism. Although recent studies have noted a relationship between the gut microbiota and gout, whether the microbiota could ameliorate HUA-associated systemic purine metabolism remains unclear. In this study, we constructed a novel model of HUA in geese and investigated the mechanism by which Lactobacillus rhamnosus GG (LGG) could have beneficial effects on HUA. The administration of antibiotics and fecal microbiota transplantation (FMT) experiments were used in this HUA goose model. The effects of LGG and its metabolites on HUA were evaluated in vivo and in vitro. Heterogeneous expression and gene knockout of LGG revealed the mechanism of LGG. Multi-omics analysis revealed that the Lactobacillus genus is associated with changes in purine metabolism in HUA. This study showed that LGG and its metabolites could alleviate HUA through the gut-liver-kidney axis. Whole-genome analysis, heterogeneous expression, and gene knockout of LGG enzymes ABC-type multidrug transport system (ABCT), inosine-uridine nucleoside N-ribohydrolase (iunH), and xanthine permease (pbuX) demonstrated the function of nucleoside degradation in LGG. Multi-omics and a correlation analysis in HUA patients and this goose model revealed that a serum proline deficiency, as well as changes in Collinsella and Lactobacillus, may be associated with the occurrence of HUA. Our findings demonstrated the potential of a goose model of diet-induced HUA, and LGG and proline could be promising therapies for HUA.

Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis.

Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.

New species in Aspergillus section Usti and an overview of Aspergillus section Cavernicolarum.

Aspergillus sections Usti and Cavernicolarum are accommodated in the subgenus Nidulantes. In the present study, a polyphasic approach using morphology and multi-gene phylogeny was applied to investigate the taxonomy of these two sections. Based on the phylogenetic analysis, Aspergillus section Usti includes 25 species, which can be assigned to four series: Calidousti, Deflecti, Monodiorum and Usti. Aspergillus sigarelli is newly described in this section and this species was isolated from a cigarette from PR China and belongs to series Calidousti. It is clearly distinct from other members in this series based on ITS, BenA, CaM and RPB2 sequences. Aspergillus section Usti members like A. calidoustus and A. granulosus are important opportunistic pathogens, it is speculative that more pathogenetic species will be found by using polyphasic taxonomy approaches. Aspergillus section Cavernicolarum includes five species, the growth rates on agar media and size and ornamentation of conidia are important characters for differentiating species in section Cavernicolarum.

New section and species in Talaromyces.

Talaromyces is a monophyletic genus containing seven sections. The number of species in Talaromyces grows rapidly due to reliable and complete sequence data contributed from all over the world. In this study agricultural soil samples from Fujiang, Guangdong, Jiangxi, Shandong, Tibet and Zhejiang provinces of China were collected and analyzed for fungal diversity. Based on a polyphasic approach including phylogenetic analysis of partial ITS, BenA, CaM and RPB2 gene sequences, macro- and micro-morphological analyses, six of them could not be assigned to any described species, and one cannot be assigned to any known sections. Morphological characters as well as their phylogenetic relationship with other Talaromyces species are presented for these putative new species. Penicillium resedanum is combined in Talaromyces section Subinflati as T. resedanus.

Penicillium section Lanata-divaricata from acidic soil.

Penicillium species in section Lanata-divaricata are common soil-inhabiting fungi, but their presence in acidic soil has rarely been investigated. In an ongoing survey of Penicillium species occurring in China, 465 strains were isolated from soil, and of which 60 belonged to section Lanata-divaricata. The majority of these strains were isolated from acidic soil. The phylogenetic relationship between these 60 isolates and accepted species of section Lanata-divaricata was studied using ITS, BenA, CaM and RPB2 sequences, which revealed the presence of seven accepted species and 13 novel lineages. Combining phylogenetic data with data generated during macro- and microscopic observations resulted in the description of 13 new species. The growth rate of the new species obtained in this study was determined under acidic, neutral and alkaline conditions (pH 4, 7, 10). With the exception of P. hainanense, which was not able to grow at pH 10, all strains were able to grow at the three examined pH levels. Eleven species (i.e. P. austrosinense, P. flaviroseum, P. globosum, P. griseoflavum, P. hainanense, P. jianfenglingense, P. laevigatum, P. rubriannulatum, P. soliforme, P. spinuliferum, P. yunnanense) grew faster at low pH (pH 4) than at pH 7 or 10, and these species are therefore referred to as acid-preferential. Penicillium viridissimum grew fastest on neutral medium and P. guangxiense grew best at pH 10, and is therefore considered to be acid-tolerant. By isolating strains from a unique environment, combined with targeted isolation using a well-designed protocol, we are able to describe new fungal diversity with specific physiological characteristics.

Three new species of Talaromyces sect. Talaromyces discovered from soil in China.

Three new Talaromyces species isolated from soil are reported here, namely T. dimorphus (ex-type strain AS3.15692 T), T. lentulus (ex-type strain AS3.15689 T) and T. mae (ex-type strain AS3.15690 T). T. dimorphus is characterized by biverticillate and monoverticillate penicilli, ampulliform phialides, slimy texture with sparse mycelial funicles and absent conidiogenesis on MEA. T. lentulus is featured by vivid yellow mycelium on Cz and MEA, absent conidiogenesis on CYA, and globose smooth-walled conidia. T. mae presents sparse conidia on CYA and YES, funiculous and floccose texture on MEA, and ovoid smooth-walled conidia. Both morphological and molecular characters show that T. dimorphus is unique and has no close relatives. Although T. lentulus and T. mae resembles T. adpressus and T. pinophilus very much, phylogenetic analyses of CaM, BenA, ITS and Rpb2 sequences all support their status as novel species.