Next‐generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development

Dampness and visible mold in homes are associated with asthma development, but causal mechanisms remain unclear. The goal of this research was to explore associations among measured dampness, fungal exposure, and childhood asthma development without the bias of culture‐based microbial analysis. In the low‐income, Latino CHAMACOS birth cohort, house dust was collected at age 12 months, and asthma status was determined at age 7 years. The current analysis included 13 asthma cases and 28 controls. Next‐generation DNA sequencing methods quantified fungal taxa and diversity. Lower fungal diversity (number of fungal operational taxonomic units) was significantly associated with increased risk of asthma development: unadjusted odds ratio (OR) 4.80 (95% confidence interval (CI) 1.04–22.1). Control for potential confounders strengthened this relationship. Decreased diversity within the genus Cryptococcus was significantly associated with increased asthma risk (OR 21.0, 95% CI 2.16–204). No fungal taxon (species, genus, class) was significantly positively associated with asthma development, and one was significantly negatively associated. Elevated moisture was associated with increased fungal diversity, and moisture/mold indicators were associated with four fungal taxa. Next‐generation DNA sequencing provided comprehensive estimates of fungal identity and diversity, demonstrating significant associations between low fungal diversity and childhood asthma development in this community.     

Electricity generation and microbial community structure of air-cathode microbial fuel cells powered with the organic fraction of municipal solid waste and inoculated with different seeds

The organic fraction of municipal solid waste (OFMSW), normally exceeding 60% of the waste stream in developing countries, could constitute a valuable source of feed for microbial fuel cells (MFCs). This study tested the start-up of two sets of OFMSW-fed air-cathode MFCs inoculated with wastewater sludge or cattle manure. The maximum power density obtained was 123 ± 41 mW m⁻² in the manure-seeded MFCs and 116 ± 29 mW m⁻² in the wastewater-seeded MFCs. Coulombic efficiencies ranged between 24 ± 5% (manure-seeded MFCs) and 23 ± 2% (wastewater-seeded MFCs). Chemical oxygen demand removal was >86% in all the MFCs and carbohydrate removal >98%. Microbial community analysis using 16S rRNA gene pyrosequencing demonstrated the dominance of the phylum Firmicutes (67%) on the anode suggesting the possible role of members of this phylum in electricity generation. Principal coordinate analysis showed that the microbial community structure in replicate MFCs converged regardless of the inoculum source. This study demonstrates efficient electricity production coupled with organic treatment in OFMSW-fueled MFCs inoculated with manure or wastewater.     

Microbial Diversity of Ground Beef Products in South Korean Retail Market Analyzed by PCR-DGGE and 454 Pyrosequencing

The purpose of this study was to assess the microbial community in ground beef purchased from local stores in the north central area of South Korea. A total of 31 ground beef samples showed 3.77 ± 5.16 × 10⁵ CFU/g on aerobic plate counts, and PCR-based denaturing gradient gel electrophoresis was performed to assess the microbial community, which revealed a diverse profile among the products. Four of these samples were selected for further analyses via 454 pyrosequencing. Pseudomonas was the most frequently identified genus in terms of relative abundance (4.54–73.8%), and other bacteria such as Lactobacillus, Acinetobacter, and Carnobacterium were also identified in the ground beef. The presence of bacteria can affect the spoilage of ground beef products depending on the microbial populations, and understanding these populations may help limit spoilage and/or foodborne illness. This study illustrates the microbial diversity occurring among Korean ground beef products, even within a local region, and provides a molecular approach for potential ground beef microbial quality assessment.     

Tetra-Repeat Microsatellite Markers for the Masu Salmon (Oncorhynchus masou masou) and Its Application in Cross-Subspecies Amplification

We developed tetranucleotide-repeat microsatellite markers for the masu salmon (Oncorhynchus masou) complex. 454 pyrosequencing was used to discover repeat motifs, and seven polymorphic microsatellite-primer sets were identified. The number of alleles detected at each locus ranged from four to 24 and the expected heterozygosity varied from 0.57 to 0.92. Cross-subspecies amplification for O. m. masou, O. m. ishikawae and O. m. subsp. was successful. These microsatellites can be utilized in studies of genetic structure, genetic diversity, and intra- and inter-subspecific hybridization, making a contribution to conservation and management of the Oncorhynchus masou complex.     

Cereal‐based fermented foods in developing countries: ancient foods for modern research

Cereal‐based fermented foods are major contributors to energy intake in developing countries (DC). Their microbiota is dominated by lactic acid bacteria and has been extensively investigated. Diversity studies have been facilitated by molecular methods enabling genotyping of isolates; the rapid development of ‘omics’ approaches should facilitate more comprehensive studies to describe the relation between microbial diversity, cell physiology and product characteristics. Also, the link between the food microbiota and health benefits, in particular in nutrition, should be investigated. There is a need to encourage researches in the field of DC cereal‐based foods in direction of more mechanistic approaches.     

Next‐Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China

Fermented soybean foods contain nutritional components including easily digestible peptides, cholesterol‐free oils, minerals, and vitamins. Various fermented soybean foods have been developed and are consumed as flavoring condiments in Asian regions. While the quality of fermented soybean foods is largely affected by microorganisms that participate in the fermentation process, our knowledge about the microorganisms in soybean pastes manufactured in Northeast China is limited. The current study used a culture‐independent barcoded pyrosequencing method targeting hypervariable V1/V2 regions of the 16S rRNA gene to evaluate Korean doenjang and soybean pastes prepared by the Hun Chinese (SPHC) and Korean minority (SPKM) populations in Northeast China. In total, 63399 high‐quality sequences were derived from 16 soybean paste samples collected in Northeast China. Each bacterial species‐level taxon of SPHC, SPKM, and Korean doenjang was clustered separately. Each paste contained representative bacterial species that could be distinguished from each other: Bacillus subtilis in SPKM, Tetragenococcus halophilus in SPHC, and Enterococcus durans in Korean doenjang. This is the 1st massive sequencing‐based study analyzing microbial communities in soybean pastes manufactured in Northeast China, compared to Korean doenjang. Our results clearly showed that each soybean paste contained unique microbial communities that varied depending on the manufacturing process and location.     

基于16S rRNA基因V3-V4区高通量测序分析东北自然发酵酸菜中细菌群落结构

为探究东北自然发酵酸菜中细菌群落结构,本试验采用454 FLX+平台对东北地区传统自然发酵的16份酸菜汁样品中细菌16S rRNA基因的V3-V4区进行测序。通过454焦磷酸测序,共得到302327条有效序列。计算Chao 1指数、Shannon指数和Simpson指数,对样品菌群的Alpha多样性进行评价,发现松原和大庆样品的细菌群落具有较高的丰富度。Beta多样性分析发现黑龙江、吉林和辽宁省份样品中存在交叠细菌物种,但含量极低。Heatmap图显示各省份的优势菌属各不相同。样品群落结构分析表明大庆、黑河和松原样品中乳杆菌含量超过50%,黑河样品中乳杆菌含量高达69.6%。KEGG统计结果表明高纬度地区存在着一定数量的耐寒细菌。此外,本试验首次在发酵食品中发现污蝇解壳杆菌属细菌(wohlfahrtiimonas),显示出高通量测序技术相对传统纯培养技术的优势。     

化学竹浆废水活性污泥细菌菌群结构分析

本研究利用超高通量基因组454测序技术分析实际化学竹浆废水活性污泥中的细菌菌群结构和多样性,分析表明,不同竹浆废水处理厂废水香农指数为4.48～5.19,ACE指数为767.80～1066.15,进一步得到不同化学竹浆废水活性污泥细菌菌群不仅具备多样性,同时具有较为显著的差异性。结果表明,化学竹浆废水活性污泥中比较常见的菌门包括Proteobacteria (变形菌门)、Chloroflexi (绿弯菌门)、Bacteroidetes (拟杆菌门)和Actinobacteria (放线菌门),其中Proteobacteria(变形菌门)占主导地位,最高丰度为59.47%;主要属为Hyphomicrobium (生丝微菌属)、Candidatus_Competibacter、JdFR-76和SWB02,其中生丝微菌属占主导地位,丰度为3.69%～18.29%。这些菌属不仅与硝化和反硝化过程相关,还与多环芳香族类化合物、醇类及烷烃类物质的降解直接有关。