Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis

Applied Microbiology and Biotechnology - Weaning stress has serious negative effects on piglets’ health and the swine industry. Probiotics-fermented Chinese herbal medicines are potential...     

Processing Mechanism of Massa Medicata Fermentata Based on the Correlation Analysis of Strains,Chemical Compositions and Anti-Inflammatory Activity

The traditional Chinese medicine of fermented medicine may be under the involvement of multiple strains and the interaction between these microorganisms. Liu Shenqu (Massa Medicata Fermentata, MMF) is one of the most widely used fermented medicines, whose potential processing mechanism is still unclear. In this work, UPLC/MS and GNPS methods were employed to rapidly predict chemical compositions in MMF. Moreover, the dynamic changes of strains, chemical compositions and anti-inflammatory activity of MMF during fermentation process were investigated, and subsequently strains-chemical compositions-efficacy interactions were revealed by Pearson correlation analysis and partial least squares regression (PLSR) analysis. As a result, 24 components were identified, and the potential strains including Bacillus, Burkholderia_Caballeronia_Paraburkholderia, Enterobacter, Aspergillus heterocaryoticus, Rhizopus arrhizus, Kazachstania bulderi, which related to the production of anti-inflammatory active ingredients were exposed. These results demonstrated chemical compositions-strains-efficacy interactions during fermentation of MMF, and provide reference for the exploration of the processing mechanism of MMF.     

Monitoring the bacterial population dynamics in sourdough fermentation processes by using PCR-denaturing gradient gel electrophoresis

Four sourdoughs (A to D) were produced under practical conditions by using a starter mixture of three commercially available sourdough starters and a baker's yeast constitutively containing various species of lactic acid bacteria (LAB). The sourdoughs were continuously propagated until the composition of the LAB flora remained stable. Two LAB-specific PCR-denaturing gradient gel electrophoresis (DGGE) systems were established and used to monitor the development of the microflora. Depending on the prevailing ecological conditions in the different sourdough fermentations, only a few Lactobacillus species were found to be competitive and became dominant. In sourdough A (traditional process with rye flour), Lactobacillus sanfranciscensis and a new species, L. mindensis, were detected. In rye flour sourdoughs B and C, which differed in the process temperature, exclusively L. crispatus and L. pontis became the predominant species in sourdough B and L. crispatus, L. panis, and L. frumenti became the predominant species in sourdough C. On the other hand, in sourdough D (corresponding to sourdough C but produced with rye bran), L. johnsonii and L. reuteri were found. The results of PCR-DGGE were consistent with those obtained by culturing, except for sourdough B, in which L. fermentum was also detected. Isolates of the species L. sanfranciscensis and L. fermentum were shown by randomly amplified polymorphic DNA-PCR analysis to originate from the commercial starters and the baker's yeast, respectively.     

Bacterial biodiversity and dynamics during malolactic fermentation of Tempranillo wines as determined by a culture-independent method (PCR-DGGE)

The bacterial population during malolactic fermentation of Tempranillo wine was studied using the polymerase chain reaction-denaturing gradient gel electrophoresis, a culture-independent method successfully used for identification and monitoring of bacterial population in different habitats included food fermentations. The results showed that Oenococcus oeni was the predominant species in the malolactic fermentation of Tempranillo wines, although the presence of Gluconobacter oxydans, Asaia siamensis, Serratia sp., and Enterobacter sp. was also observed. These results were partly coincidental with those obtained from a culture-dependent method, using a selective medium. Therefore, it may be concluded that for a more complete knowledge of the bacterial community present during malolactic fermentation of Tempranillo wine, an approach that combines a culture-independent method and a culture-dependent method would be advisable.     

Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition

In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.     

Temperature variation,bacterial diversity and fungal infection dynamics in the amphibian skin

Host‐associated bacterial communities on the skin act as the first line of defence against invading pathogens. Yet, for most natural systems, we lack a clear understanding of how temperature variability affects structure and composition of skin bacterial communities and, in turn, promotes or limits the colonization of opportunistic pathogens. Here, we examine how natural temperature fluctuations might be related to changes in skin bacterial diversity over time in three amphibian populations infected by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Our focal host species (Eleutherodactylus coqui) is a direct‐developing frog that has suffered declines at some populations in the last 20 years, while others have not experienced any changes. We quantified skin bacterial alpha‐ and beta‐diversity at four sampling time points, a period encompassing two seasons and ample variation in natural infections and environmental conditions. Despite the different patterns of infection across populations, we detected an overall increase in bacterial diversity through time, characterized by the replacement of bacterial operational taxonomic units (OTUs). Increased frog body temperatures possibly allowed the colonization of bacteria as well as the recruitment of a subset of indicator OTUs, which could have promoted the observed changes in diversity patterns. Our results suggest that natural environmental fluctuations might be involved in creating opportunities for bacterial replacement, potentially attenuating pathogen transmission and thus contributing to host persistence in E. coqui populations.     

Studying the dynamics of microbial populations during food fermentation

The dynamics of growth, survival and biochemical activity of microorganisms in food are the result of stress reactions in response to the changing of the physical and chemical conditions into the food microenvironment, the ability to colonise the food matrix and to growth into a spatial heterogeneity, and the in situ cell-to-cell ecological interactions which often happen in a solid phase. In food, ecological approaches to study the evolution of microbial flora would be useful to comprehend better the microbiological processes involved in food processing and ripening, to improve microbiological safety by monitoring in situ pathogenic bacteria, and to evaluate the effective compositions of the microbial populations. This paper gives a general overview of biotechnological approaches to study microbial populations in food fermentation.     

Taxol from fungal endophytes and the issue of biodiversity

Fungi represent one of the most understudied and diverse group of organisms. Commonly, these organisms make associations with higher life forms and may proceed to biochemically mimic the host organism. An excellent example of this is the anticancer drug, taxol, which had been previously supposed to occur only in the plant genusTaxus (yew). However, taxol has been reported in a novel endophytic fungus—Taxomyces andreanae, but also has been demonstrated to occur in a number of unrelated fungal endophytes includingPestalotia, Pestalotiopsis, Fusarium, Alternaria, Pithomyces, Monochaetia and others. Thus, this report presents information on the presence of taxol among disparate fungal genera, and uses these observations as an additional argument to support efforts to study fungal endophytes and preserve their associated host plants.     

Dynamics of bacterial and fungal communities associated with eggshells during incubation

Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture‐based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival.     

Monitoring the bacterial community during fermentation of sunki, an unsalted, fermented vegetable traditional to the Kiso area of Japan

Aims:  To investigate the microbial community in sunki , an indigenous, unsalted, fermented vegetable, made from the leaves of red beet.
Methods and Results:  Fermenting samples were collected at 1- to 2-day intervals from four houses and investigated by culture-dependent and culture-independent techniques. PCR-Denaturing-Gradient-Gel-Electrophoresis profiles indicated that the bacterial community was stable and Lactobacillus delbrueckii , Lact. fermentum and Lact. plantarum were dominant during the fermentation. This result agreed well with that obtained by the culturing technique. Moulds, yeasts or bacteria other than lactic acid bacteria (LAB) were not detected.
Conclusions:  The bacterial community was stable throughout the fermentation, and Lact. delbrueckii , Lact. fermentum and Lact. plantarum were dominant. The acidic pH and lactic acid produced by LAB probably preserve the sunki from spoilage.
Significance and Impact of the Study:  This is the first report on the use of both culture-dependent and culture-independent techniques to study the bacterial community in sunki . A combination of culture-dependent and culture-independent techniques is necessary for the analysis of complex microbial communities.     

Yeast population dynamics during the fermentation and biological aging of sherry wines

Molecular and physiological analyses were used to study the evolution of the yeast population, from alcoholic fermentation to biological aging in the process of "fino" sherry wine making. The four races of "flor" Saccharomyces cerevisiae (beticus, cheresiensis, montuliensis, and rouxii) exhibited identical restriction patterns for the region spanning the internal transcribed spacers 1 and 2 (ITS-1 and ITS-2) and the 5.8S rRNA gene, but this pattern was different, from those exhibited by non-flor S. cerevisiae strains. This flor-specific pattern was detected only after wines were fortified, never during alcoholic fermentation, and all the strains isolated from the velum exhibited the typical flor yeast pattern. By restriction fragment length polymorphism of mitochondrial DNA and karyotyping, we showed that (i) the native strain is better adapted to fermentation conditions than commercial strains; (ii) two different populations of S. cerevisiae strains are involved in the process of elaboration, of fino sherry wine, one of which is responsible for must fermentation and the other, for wine aging; and (iii) one strain was dominant in the flor population integrating the velum from sherry wines produced in González Byass wineries, although other authors have described a succession of races of flor S. cerevisiae during wine aging. Analyzing all these results together, we conclude that yeast population dynamics during biological aging is a complex phenomenon and differences between yeast populations from different wineries can be observed.     

High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation

We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITS-RFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods for studying the yeast community on grapes and during alcoholic fermentation. Indeed, this high-throughput sequencing method detected larger numbers of species on grapes and identified species present during alcoholic fermentation that were undetectable with the other techniques.     

An enzyme-linked immunosorbent assay for the estimation of fungal biomass during solid-state fermentation

An enzyme-linked immunosorbent assay for sensitive, specific and quantitative estimation of fungal biomass during solid-state fermentation is described. Using this method, differential growth rates and colonization of the substrate can be studied. The assay has potential application for the efficient monitoring of solid-state fermentation involving specific fungus, for which available methods are not adequate. Received: 18 November 1997 / Received last revision: 8 June 1998 / Accepted: 14 June 1998     

Diversity and dynamics stability of bacterial community in traditional solid-state fermentation of Qishan vinegar

Qishan vinegar is a typical Chinese fermented cereal product that is prepared using traditional solid-state fermentation (SSF) techniques. The final qualities of the vinegar produced are closely related to the multiple bacteria present during SSF. In the present study, the dynamics of microbial communities and their abundance in Daqu and vinegar Pei were investigated by the combination of high throughput sequencing and quantitative PCR. Results showed that the Enterobacteriales members accounted for 94.7%, 94.6%, and 92.2% of total bacterial sequences in Daqu Q3, Q5, and Q10, respectively. Conversely, Lactobacillales and Rhodospirillales dominated during the acetic acid fermentation (AAF) stage, corresponding to the quantitative PCR results. Lactobacillus, Acetobacter, Weissella, Leuconostoc and Bacillus were the dominant and characteristic bacterial genera of Qishan vinegar during AAF process. Redundancy analysis suggested that Lactobacillales and Rhodospirillales had a positive correlation with humidity and acidity, respectively. These results confirmed that the bacterial community structure could be affected by physiochemical factors, which determined the unique bacterial composition at different fermentation stages and showed batch-to-batch consistency and stability. Therefore, the conformity of bacterial community succession with physiochemical parameters guaranteed the final quality of Qishan vinegar products. This study provided a scientific perspective for the uniformity and stability of Qishan vinegar, and might aid in controlling the manufacturing process.     

真菌资源与多样性专刊序言

正"地球上有多少物种?"是最具挑战性的前沿科学问题之一。真菌是仅次于昆虫的第二大生物类群,据估计自然界中真菌有220万到380万种,目前已经描述的真菌仅约12万种,不超过总数的8%。现代的高通量测序技术运用于真菌多样性的研究揭示自然环境中蕴含的真菌多样性甚至可能远远高于我们原先的估计。对于真菌多样性的研究,仍任重道远。我国对真菌的认识     

全球生物多样性监测及其进展

全球生物多样性监测及其进展曹志平（中国农业大学资环学院生态系,北京１０００９４）钟晓东（国家环保局国际合作司,北京１０００３５）１背景生物多样性监测最主要的目的是为管理者和决策者服务［１］,为他们在保护生物多样性、制定土地利用规划、评价环境影响等问...     

Modeling Grifola frondosa fungal growth during solid‐state fermentation

Grifola frondosa (maitake) is an edible and medicinal mushroom. Considering its increasing popularity, there are limited references for its cultivation. Previous studies demonstrated that carpophore formation is correlated directly with mycelial biomass. The development of a mathematical model for its growth under solid‐state fermentation (SSF) may help to predict the potential of different substrates for maitake production. G. frondosa growth and basidiome development was studied, using oak sawdust and corn bran as substrates. The fungal biomass content was determined by measuring N‐acetyl‐D ‐glucosamine (NAGA). It increased steadily for the first 80 days, to a maximum in coincidence with the first fruiting (60.5 μg NAGA/mg dry sample). Two mathematical models were selected to evaluate G. frondosa development, measuring reducing sugars consumption and NAGA synthesis, as an indirect assessment of fungal growth. Both models showed a good fit between predicted and experimental data: logistic model (R²=0.8896), two‐stage model (R²=0.8878), but the logistic model required a minor number of adjustment parameters.     

Effects of physico-chemical parameters on the bacterial and fungal communities during agricultural waste composting

The goal of this study was to identify and prioritize some of the physico-chemical parameters that contributed to bacterial and fungal community compositions during agricultural waste composting. Relationships between those parameters and microbial community compositions determined by PCR-DGGE were simultaneously evaluated by redundancy analysis (RDA). The results showed that the temporal variation of bacterial community composition was significantly related to water soluble carbon (WSC), ammonium and nitrate (P<0.05), while the most variation in distribution of fungal community composition was statistically explained by pile temperature, WSC, and moisture content (P<0.05). Significant amounts of the variation (54.9% and 56.0% for bacterial and fungal species data, respectively) were explained by those parameters, suggesting that those parameters were the most likely ones to influence, or be influenced by the bacterial and fungal species. Variation partitioning analyses indicated that WSC and pile temperature showed predominant effect on the bacterial and fungal community composition, respectively.