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.     

Microbial composition of the Korean traditional food "kochujang" analyzed by a massive sequencing technique

Kochujang is a traditional Korean fermented food that is made with red pepper, glutinous rice, salt, and soybean. Kochujang is fermented by naturally occurring microorganisms through which it obtains various health-promoting properties. In this study, the bacterial diversities of 9 local and 2 commercial brands of kochujang were analyzed with a barcoded pyrosequencing technique targeting the hyper-variable regions V1/V2 of the 16S rRNA gene. Through the analysis of 13524 bacterial pyrosequences, 223 bacterial species were identified, most of which converged on the phylum Firmicutes (average 93.1%). All of the kochujang samples were largely populated (>90.9% of abundance) by 12 bacterial families, and Bacillaceae showed the highest abundance in all but one sample. Bacillus subtilis and B. licheniformis were the most dominant bacterial species and were broadly distributed among the kochujang samples. Each sample contained a high abundance of region-specific bacterial species, such as B. sonorensis, B. pumilus, Weissella salipiscis, and diverse unidentified Bacillus species. Phylotype- and phylogeny-based community comparison analysis showed that the microbial communities of the two commercial brands were different from those of the local brands. Moreover, each local brand kochujang sample had region-specific microbial community reflecting the manufacturing environment.     

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.     

原核微生物菌群的空间分异增强秸秆-猪粪混合发酵效率

秸秆与禽畜粪便混合发酵既可增强反应器稳定性又能提高发酵产气效率。然而关于秸秆附着菌群、发酵液菌群的时空动态变化,以及它们与产气效率、环境变量的关系仍然未被全部揭示。采用16S rRNA基因扩增子高通量测序技术,对这一问题进行了研究。结果显示,秸秆猪粪混合发酵能够改善沼气发酵的效率。原核微生物群落在空间上的差异分布可能有助于提升系统的效率。在产气高效的系统中,秸秆吸附菌群如Treponema、Clostridium Ⅲ、Alkaliflexus 和 Fibrobacter是主要的纤维素降解菌,提供底物给产酸菌。丙酸是发酵液中含量最丰富的挥发性脂肪酸（VFAs）,Pelotomaculum可能是该系统主要的丙酸氧化菌,它们与Methanoculleus、Methanosarcina和Methanosaeta协同作用通过二氧化碳/氢营养型和乙酸营养型产甲烷途径,将包括丙酸在内的VFAs最终转化成甲烷。参与氨基酸代谢的Aminobacterium和Cloacibacillus广泛分布于发酵液中,表明蛋白质是一种重要的发酵底物,说明VFAs尤其是丙酸和氨基酸的互营代谢可能是秸秆猪粪混合发酵系统的重要过程。这些结果表明,功能菌群的空间分化、稳定的秸秆降解菌群和发酵液菌群的弹性变化有助于维持秸秆猪粪混合发酵系统的稳定性和提高发酵效率。     

Development of Microsatellite Markers Using Pyrosequencing in Galium trifidum (Rubiaceae), a Rare Species in Central Europe

We identify a large number of microsatellites from Galium trfidum, a plant species considered rare and endangered in Central and Western Europe. Using a combination of a total enriched genomic library and small-scale 454 pyrosequencing, we determined 9755 contigs with a length of 100 to 6192 bp. Within this dataset, we identified 153 SSR motifs in 144 contigs. Here, we tested 14 microsatellite loci in 2 populations of G. trifidum. The number of alleles and expected heterozygosity were 1-8 (mean 3.2) and 0.00-0.876 (0.549 on average), respectively. The markers described in this study will be useful for evaluating genetic diversity within and between populations, and gene flow between G. trifidum populations. These markers could also be applied to investigate the biological aspects of G. trifidum, such as the population dynamics and clonal structure, and to develop effective conservation programs for the Central European populations of this species.     

焦磷酸测序法分析中国荷斯坦牛、娟姗牛及 水牛的乳蛋白基因多态性

目的 本研究旨在分析和比较中国荷斯坦牛、娟姗牛和水牛的乳蛋白基因多态性。方法 根据奶牛多态位点设计引物, 采用焦磷酸测序法分析乳蛋白基因多态性, 并采用高效液相色谱法进行验证。结果 荷斯坦牛和娟姗牛的乳蛋白(β-casein, κ-casein和β-lactoglobulin)均存在基因多态性, 而水牛仅在κ-casein上存在多态性且多态位点与另两种奶牛不同。结论 中国荷斯坦牛、娟姗牛和水牛的乳蛋白基因均存在多态性, 焦磷酸测序法能高通量、快速测定乳蛋白基因多态性。     

16S rRNA pyrosequencing-based investigation of the bacterial community in nukadoko, a pickling bed of fermented rice bran

Nukadoko is a naturally fermented rice bran mash traditionally used for pickling vegetables in Japan; its refreshment and fermentation cycles sometimes continue for many years. Here, we investigated the structure and dynamics of the bacterial community in nukadoko by conducting pyrosequencing and quantitative polymerase chain reaction (PCR) analyses of 16S ribosomal RNA genes (rDNA). Of the 16 different samples studied, 13 showed Lactobacillus-dominated microbiota, suggesting that aged nukadoko samples tend to realize a niche, favorable Lactobacillus species. The lactic acid bacterial community of each of the 16 samples was classified into 3 types according to the presence or absence of 2 predominant species, Lactobacillus namurensis and Lactobacillus acetotolerans. The dynamics of the bacterial community during fermentation and the subsequent ripening process were examined using a laboratory model of nukadoko inoculated with an aged nukadoko sample (inoculated model). Lb. namurensis grew rapidly in the first 2 days, accompanied with a rapid decrease in pH and an increase in lactate levels, while Lb. acetotolerans grew with a longer doubling time and slow acidification during the 20 days after inoculation. On the other hand, spontaneous fermentation of the nukadoko model prepared from fresh rice bran without the nukadoko inoculation (inoculant-free model), showed the growth of some non-Lactobacillus species such as staphylococci and bacilli within the first 10 days; thereafter, Lb. namurensis was dominant, while Lb. acetotolerans was not detected during the 20-day experimental period. These results suggest that the naturally established Lactobacillus community in aged nukadoko is effectively involved in the biocontrol of the microbial community of nukadoko during the refreshment and fermentation cycles.