Community Dynamics of Bacteria in Sourdough Fermentations as Revealed by Their Metatranscriptome

also had the highest number of high-molecular-mass glutenins. Type I sourdoughs were prepared at the laboratory level through a back-slopping procedure, and the bacterial ecology during sourdough preparation was described by 16S rRNA gene pyrosequencing. Before fermentation, the dough made with C ONV flour showed the highest bacterial diversity. Flours were variously contaminated by genera belonging to the Proteobacteria, Firmicutes, and Actinobacteria. Mature sourdoughs were completely and stably dominated by lactic acid bacteria. The diversity of Firmicutes was the highest for mature sourdoughs made with organic and, especially, NO INPUT flours. Beta diversity analysis based on the weighted UniFrac distance showed differences between doughs and sourdoughs. Those made with C ONV flour were separated from the other with organic flours. Lactic acid bacterium microbiota structure was qualitatively confirmed through the culturing method. As shown by PCR-denaturing gradient gel electrophoresis (DGGE) analysis, yeasts belonging to the genera Saccharomyces, Candida, Kazachstania, and Rhodotorula occurred in all sourdoughs. Levels of bound phenolic acids and phytase and antioxidant activities differed depending on the farming system. Mature sourdoughs were used for bread making. Technological characteristics were superior in the breads made with organic sourdoughs. The farming system is another determinant affecting the sourdough microbiota. The organic cultivation of durum wheat was reflected along the flour-sourdough fermentation-bread axis. O rganic farming is gaining broad recognition as a system that complies well with sustainability, an overarching principle that should drive agriculture now and in the coming year (1). Under organic farming practices, crops grow without using chemical pesticides, herbicides, and fertilizers and the cultivation relies mainly on crop rotation, compost, and green manure (e.g., N 2 -fixing plants), organic fertilizers, and plant-based pesticides. Raw materials or foods, which are sold as organics in the European Union (EU), have to be produced strictly respecting European legislation (2). Based on these characteristics and constraints, consumers perceived organic foods as healthier and more eco-sustainable than conventional ones (3). In the period 2006 through 2010, certified organic production in Europe has increased by more than 40% (4). According to the Italian Institute for Food and Agricultural Market, organic farming in Italy contributes to over 25% of the organically cultivated products in Europe (5).Cereals represent the most important organic food category, with 18% of all EU organic land and ca. 80% of the total organic arable crop area (4). Among cereals, organic and conventional durum wheat (Triticum turgidum subsp. durum) is cultivated on over 3.7 million ha in the EU, and more than one-half of this acreage lies in the Mediterranean area, wherein Italy and Spain are the first and second top producers (6). In Italy, ca. 67% of the production of durum wheat comes from the ...

Section: Discussionmentioning

confidence: 99%

Organic Cultivation of Triticum turgidum subsp. durum Is Reflected in the Flour-Sourdough Fermentation-Bread Axis

Rizzello

Cavoski

Turk

et al. 2015

“…Until recently, metatranscriptomics had been limited to the microarray/high-density array technology (46,86,140) or analysis of mRNA-derived cDNA clone libraries (90,119). These approaches have produced significant insights into the gene expression of microbial communities but have limitations.…”

Section: Metatranscriptomicsmentioning

confidence: 99%

Metagenomic Analyses: Past and Future Trends

Simon

Daniel

2011

607

349

Metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body, and ocean water. Analyses of these data sets opened a window into the enormous taxonomic and functional diversity of environmental microbial communities. To assess the functional dynamics of microbial communities, metatranscriptomics and metaproteomics have been developed. The combination of DNA-based, mRNA-based, and protein-based analyses of microbial communities present in different environments is a way to elucidate the compositions, functions, and interactions of microbial communities and to link these to environmental processes.

“…Lactobacillus plantarum and Lactobacillus spicheri dominated in the bakery environment and in the sourdough produced in the same bakery (17). Evidence has indicated that sourdough fermentations carried out in the laboratory with the flour as the only nonsterile ingredient were characterized by species and/or strains of lactic acid bacteria different from those in artisan sourdoughs (14,(19)(20)(21)(22). This would suggest that the flour microbiota shares very few taxa with that of the corresponding mature sourdough.…”

mentioning

confidence: 99%

Lactic Acid Bacteria in Durum Wheat Flour Are Endophytic Components of the Plant during Its Entire Life Cycle

Minervini

Celano

Lattanzi

et al. 2015

100

bThis study aimed at assessing the dynamics of lactic acid bacteria and other Firmicutes associated with durum wheat organs and processed products. 16S rRNA gene-based high-throughput sequencing showed that Lactobacillus, Streptococcus, Enterococcus, and Lactococcus were the main epiphytic and endophytic genera among lactic acid bacteria. Bacillus, Exiguobacterium, Paenibacillus, and Staphylococcus completed the picture of the core genus microbiome. The relative abundance of each lactic acid bacterium genus was affected by cultivars, phenological stages, other Firmicutes genera, environmental temperature, and water activity (a w ) of plant organs. Lactobacilli, showing the highest sensitivity to a w , markedly decreased during milk development (Odisseo) and physiological maturity (Saragolla). At these stages, Lactobacillus was mainly replaced by Streptococcus, Lactococcus, and Enterococcus. However, a key sourdough species, Lactobacillus plantarum, was associated with plant organs during the life cycle of Odisseo and Saragolla wheat. The composition of the sourdough microbiota and the overall quality of leavened baked goods are also determined throughout the phenological stages of wheat cultivation, with variations depending on environmental and agronomic factors.