scholarly journals Microbial community dispersal in sourdough

2021 ◽  
Author(s):  
Lucas von Gastrow ◽  
Remy Amelot ◽  
Diego Segond ◽  
Stephane Guezennec ◽  
Florence Valence ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Microbial Community ◽  
Lactic Acid Bacteria ◽  
Microbial Communities ◽  
16S Rdna ◽  
Yeast Species ◽  
Sequence Variant ◽  
Sourdough Yeast

Understanding how microbes disperse in ecosystems is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about the vectors that may contribute to their migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal among French sourdoughs and flours used to make bread. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analyzed whether flour is a carrier of sourdough yeast and bacteria and studied whether microbial migration occurs between sourdoughs. The microbial community of a collection of 46 sourdough samples, as well as that of the flour from which each was made, was studied by 16S rDNA and ITS1 metabarcoding. No sourdough yeast species were detected in the flours. Sourdough lactic acid bacteria (LAB) were found in only five flour samples, and they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. The species shared between the sourdough and flour samples are commonly found on plants and are not known to be alive in sourdough. Thus, the flour microorganisms did not appear to grow in the sourdough microbial community. Dispersal between sourdoughs was also studied. Sourdoughs shared no yeast ASV, except in few cases where groups of three to five bakers shared some. These results suggest that there is little migration between sourdoughs, except in a few situations where bakers may exchange sourdough or be vectors of yeast dispersal themselves.

scholarly journals Interactions between Kazachstania humilis Yeast Species and Lactic Acid Bacteria in Sourdough

2020 ◽  
Vol 8 (2) ◽  
pp. 240 ◽  
Author(s):  
Belén Carbonetto ◽  
Thibault Nidelet ◽  
Stéphane Guezenec ◽  
Marc Perez ◽  
Diego Segond ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Population Density ◽  
Population Size ◽  
Yeast Species ◽  
Positive Interactions ◽  
Composition And Structure ◽  
Density Analysis ◽  
Sourdough Yeast

Sourdoughs harbor simple microbial communities usually composed of a few prevailing lactic acid bacteria species (LAB) and yeast species. However, yeast and LAB found in sourdough have been described as highly diverse. Even if LAB and yeast associations have been widely documented, the nature of the interactions between them has been poorly described. These interactions define the composition and structure of sourdough communities, and therefore, the characteristics of the final bread product. In this study, the nature of the interactions between strains of two commonly found sourdough yeast species, Kazachstania humilis and Saccharomyces cerevisiae, and lactic acid bacteria isolated from sourdoughs has been analyzed. Population density analysis showed no evidence of positive interactions, but instead revealed neutral or negative asymmetric interaction outcomes. When in coculture, the yeasts´ population size decreased in the presence of LAB regardless of the strain, while the LAB´s population size was rarely influenced by the presence of yeasts. However, a higher maltose depletion was shown in maltose-negative K. humilis and maltose-positive obligately heterofermentative LAB cocultures compared to monocultures. In addition, tested pairs of obligately heterofermentative LAB and K. humilis strains leavened dough as much as couples of LAB and S. cerevisiae strains, while K. humilis strains never leavened dough as much as S. cerevisiae when in monoculture. Taken together, our results demonstrate that even if higher fermentation levels with increased maltose depletion were detected for K. humilis and obligately heterofermentative LAB pairs, these interactions cannot be ecologically classified as positive, leading us to rethink the established hypothesis of coexistence by facilitation in sourdoughs.

scholarly journals 16S rDNA Genotyping of Lactic Acid Bacteria Using PCR-RFLP Analysis

2017 ◽  
Vol 64 (7) ◽  
pp. 355-364
Author(s):  
Hideyuki Tamakawa ◽  
Yoshihito Ito
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rdna ◽  
Rflp Analysis ◽  
Pcr Rflp

scholarly journals Relationships between Microbial Community Structure and Hydrochemistry in a Landfill Leachate-Polluted Aquifer

2001 ◽  
Vol 67 (10) ◽  
pp. 4619-4629 ◽  
Author(s):  
Wilfred F. M. Röling ◽  
Boris M. van Breukelen ◽  
Martin Braster ◽  
Bin Lin ◽  
Henk W. van Verseveld
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Microbial Community Structure ◽  
Landfill Leachate ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Numerical Comparison ◽  
Gram Positive ◽  
Gram Positive Bacteria

ABSTRACT Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria andArchaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the β subclass of the class Proteobacteria(β-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of δ-proteobacteria strongly increased and β-proteobacteria reappeared. The β-proteobacteria (Acidovorax,Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the familyGeobacteraceae made a strong contribution to the microbial communities. Because the only known aromatic hydrocarbon-degrading, iron-reducing bacteria areGeobacter spp., their occurrence in landfill leachate-contaminated aquifers deserves more detailed consideration.

scholarly journals Dynamics and Complexity of Dark Fermentation Microbial Communities Producing Hydrogen From Sugar Beet Molasses in Continuously Operating Packed Bed Reactors

2021 ◽  
Vol 11 ◽  
Author(s):  
Anna Detman ◽  
Daniel Laubitz ◽  
Aleksandra Chojnacka ◽  
Ewa Wiktorowska-Sowa ◽  
Jan Piotrowski ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Hydrogen Production ◽  
Sugar Beet ◽  
Microbial Communities ◽  
Packed Bed ◽  
Dark Fermentation ◽  
Shotgun Metagenomics ◽  
Packed Bed Reactors ◽  
Beet Molasses

This study describes the dynamics and complexity of microbial communities producing hydrogen-rich fermentation gas from sugar-beet molasses in five packed-bed reactors (PBRs). The bioreactors constitute a part of a system producing hydrogen from the by-products of the sugar-beet industry that has been operating continuously in one of the Polish sugar factories. PBRs with different working volumes, packing materials, construction and inocula were tested. This study focused on analysis (based on 16S rRNA profiling and shotgun metagenomics sequencing) of the microbial communities selected in the PBRs under the conditions of high (>100 cm3/g COD of molasses) and low (<50 cm3/g COD of molasses) efficiencies of hydrogen production. The stability and efficiency of the hydrogen production are determined by the composition of dark fermentation microbial communities. The most striking difference between the tested samples is the ratio of hydrogen producers to lactic acid bacteria. The highest efficiency of hydrogen production (130–160 cm3/g COD of molasses) was achieved at the ratios of HPB to LAB ≈ 4:2.5 or 2.5:1 as determined by 16S rRNA sequencing or shotgun metagenomics sequencing, respectively. The most abundant Clostridium species were C. pasteurianum and C. tyrobutyricum. A multiple predominance of LAB over HPB (3:1–4:1) or clostridia over LAB (5:1–60:1) results in decreased hydrogen production. Inhibition of hydrogen production was illustrated by overproduction of short chain fatty acids and ethanol. Furthermore, concentration of ethanol might be a relevant marker or factor promoting a metabolic shift in the DF bioreactors processing carbohydrates from hydrogen-yielding toward lactic acid fermentation or solventogenic pathways. The novelty of this study is identifying a community balance between hydrogen producers and lactic acid bacteria for stable hydrogen producing systems. The balance stems from long-term selection of hydrogen-producing microbial community, operating conditions such as bioreactor construction, packing material, hydraulic retention time and substrate concentration. This finding is confirmed by additional analysis of the proportions between HPB and LAB in dark fermentation bioreactors from other studies. The results contribute to the advance of knowledge in the area of relationships and nutritional interactions especially the cross-feeding of lactate between bacteria in dark fermentation microbial communities.

scholarly journals Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing

2015 ◽  
Vol 64 (1) ◽  
pp. 29-36 ◽  
Author(s):  
YA-BING CHEN ◽  
DAO-LIANG LAN ◽  
CHENG TANG ◽  
XIAO-NONG YANG ◽  
JIAN LI
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Dna Extraction ◽  
Extraction Methods ◽  
16S Rdna Sequencing ◽  
Bead Beating ◽  
Rdna Sequencing ◽  
Dna Extraction Methods

To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.

scholarly journals The isolation of exopolysaccharide-producing lactic acid bacteria from lontar (Borassus flabellifer L.) sap

2020 ◽  
Author(s):  
Anik Ma'unatin ◽  
Harijono Harijono ◽  
Elok Zubaidah ◽  
Muhaimin Rifa'i
Keyword(s):  
Lactic Acid ◽  
Quantitative Analysis ◽  
Lactic Acid Bacteria ◽  
16S Rdna ◽  
Leuconostoc Mesenteroides ◽  
Dry Mass ◽  
Total Sugar ◽  
Liquid Media ◽  
High Level ◽  
One Way Anova

Background and Objectives: Lontar (Borassus flabellifer L.) is widely grown in Indonesia and one of its products is palm sap. Palm sap contains a high level of sugar, making it suitable as a medium to increase the lactic acid bacteria (LAB) production of exopolysaccharides (EPS). This study aimed to isolate the EPS-producing LAB from palm sap and evaluate its EPS production. LAB isolation was carried out on MRS agar containing 0.5% CaCO3 . Materials and Methods: The screening and production of EPS were carried out on MRS media supplemented with 10% sucrose. The molecular identification of the selected EPS-producing LAB was based on 16S rDNA. A quantitative analysis of EPS polymer dry mass and total sugar was conducted using one-way ANOVA. Results: In this study, five EPS-producing LABs were found: Fructobacillus fructosus N4, Leuconostoc mesenteroides N5, Leuconostoc mesenteroides N7, Leuconostoc mesenteroides N9, and Fructobacillus fructosus N10. The highest EPS yield in liquid media was 10.997 ± 1.591 g/L by Leuconostoc mesenteroides N7, whereas the lowest was 4.505 ± 0.459 g/L by Fructobacillus fructosus N10. Conclusion: This study found Fructobacillus fructosus strains as EPS producers that have never been reported before.

scholarly journals Schizosaccharomyces pombe: A Promising Biotechnology to Modulate Wine Composition

2018 ◽  
Author(s):  
Iris Loira ◽  
Antonio Morata ◽  
Felipe Palomero ◽  
Carmen González ◽  
José Antonio Suárez-Lepe
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Schizosaccharomyces Pombe ◽  
Biogenic Amines ◽  
Malic Acid ◽  
Urease Activity ◽  
Yeast Species ◽  
Ethyl Carbamate ◽  
Wine Composition ◽  
Ageing On Lees

There are numerous yeast species related to wine making, particularly non-Saccharomyces, that deserve special attention due to the great potential they have when it comes to making certain changes in the composition of the wine. Among them, Schizosaccharomyces pombe stands out for its particular metabolism that gives it certain abilities such as regulating the acidity of wine through maloalcoholic fermentation. In addition, this species is characterized by favouring the formation of stable pigments in the wine and releasing large quantities of polysaccharides during ageing on lees. Moreover, its urease activity and its competition for malic acid with lactic acid bacteria make it a safety tool by limiting the formation of ethyl carbamate and biogenic amines in wine. However, it also has certain disadvantages such as its low fermentation speed or the development of undesirable flavours and aromas. In this chapter, the main oenological uses of Schizosaccharomyces pombe that have been proposed in the last years will be reviewed and discussed.

scholarly journals Isolation and Identification of Lactic Acid Bacteria from Natural Whey Cultures of Buffalo and Cow Milk

Foods ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 233
Author(s):  
Rosangela Marasco ◽  
Mariagiovanna Gazzillo ◽  
Nicoletta Campolattano ◽  
Margherita Sacco ◽  
Lidia Muscariello
Keyword(s):  
Polymerase Chain Reaction ◽  
Lactic Acid ◽  
Microbial Community ◽  
Lactic Acid Bacteria ◽  
Microbial Diversity ◽  
Strain Level ◽  
Sequencing Analysis ◽  
Chain Reaction ◽  
Isolation And Identification ◽  
Polymerase Chain

In southern Italy, some artisanal farms produce mozzarella and caciocavallo cheeses by using natural whey starter (NWS), whose microbial diversity is responsible for the characteristic flavor and texture of the final product. We studied the microbial community of NWS cultures of cow’s milk (NWSc) for the production of caciocavallo and buffalo’s milk (NWSb) for the production of mozzarella, both from artisanal farms. Bacterial identification at species and strain level was based on an integrative strategy, combining culture-dependent (sequencing of the 16S rDNA, species/subspecies-specific Polymerase Chain Reaction (PCR) and clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and culture-independent (next-generation sequencing analysis, NGS) approaches. Results obtained with both approaches showed the occurrence of five species of lactic acid bacteria in NWSb (Lactococcus lactis subsp. lactis, Lactobacillus fermentum, Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus) and five species in NWSc (Lc. lactis subsp. lactis, Enterococcus faecium, and S. thermophilus, Lb. helveticus, and Lb. delbrueckii), with the last two found only by the NGS analysis. Moreover, RAPD profiles, performed on Lc. lactis subsp. lactis different isolates from both NWSs, showed nine strains in NWSb and seven strains in NWSc, showing a microbial diversity also at strain level. Characterization of the microbiota of natural whey starters aims to collect new starter bacteria to use for tracing microbial community during the production of artisanal cheeses, in order to preserve their quality and authenticity, and to select new Lactic Acid Bacteria (LAB) strains for the production of functional foods.

scholarly journals Identification and Characterization Indigenous of Lactobacillus spfrom Bovine Rumen Fluidof Slaughterhouse

2017 ◽  
Vol 3 (6) ◽  
pp. 549
Author(s):  
Tri Nurhajati ◽  
Koesnoto Soepranianondo ◽  
Widya Paramita Lokapirnasari ◽  
Adriana Monica Sahidu
Keyword(s):  
Lactic Acid ◽  
Nucleotide Sequence ◽  
Lactic Acid Bacteria ◽  
16S Rdna ◽  
Biochemical Characterization ◽  
Rumen Fluid ◽  
Lactobacillus Rhamnosus ◽  
Bovine Rumen ◽  
Pcr Method

The discovery and characterisation of indigenous lactic acid bacteria (LAB) are important for diversity microbes as candidate probiotic. This research was aimed to identify lactic acid bacteria isolate from isolation process of local bovine rumen fluid from slaughterhouse in Surabaya Indonesia. Genotypic testing was conducted by analyzing 16S rDNA and biochemical identification. DNA of sample isolate was isolated and then amplified in vitro through the PCR method. Determination of nucleotide sequence of 16S rDNA was performed with sequencing method. The result of nucleotide sequence was than compared with GenBank database. The BLAST was then applied to identify the phylogenetic tree. Based on the biochemical characterization and nucleotide sequences, that isolate was identified as Lactobacillus rhamnosus subsp TG15. The result of this research showed that L.rhamnosus subsp TG15 showed viability bacteria in MRSA as control as much as 1.1 x 108 CFU/ml, mean while in MRSA pH 2, L.rhamnosus subsp TG15 showed its viability as much as 9.3 x 106 CFU/ml. Viability of isolate on bile tolerance 0.3% was 2.4 x 107 CFU/ml). Index antagonist bacteria test on S.aureus showed inhibition diameter as much as 2.0 mm and in antagonist test on E.coli as much as 2.5 mm. Based on the result, it could be concluded that this research found a new strain of lactic acid bacteria, L.rhamnosus subsp TG15 and that isolate has ability as the probiotic candidate. Keywords: L.rhamnosus subsp TG15; survival on acidity; bile salts; S.aureus and E.coli

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