scholarly journals Zooming Into the Microbiota of Home-Made and Industrial Kefir Produced in Greece Using Classical Microbiological and Amplicon-Based Metagenomics Analyses

2021 ◽  
Vol 12 ◽  
Author(s):  
Maria Kazou ◽  
Andriana Grafakou ◽  
Effie Tsakalidou ◽  
Marina Georgalaki
Keyword(s):  
High Throughput Sequencing ◽  
Yeast Species ◽  
Debaryomyces Hansenii ◽  
Lactobacillus Delbrueckii ◽  
Microbiological Analysis ◽  
Symbiotic Association ◽  
Geographical Regions ◽  
Wide Range ◽  
Fungal Microbiota ◽  
Culture Dependent

Kefir is a high nutritional fermented dairy beverage associated with a wide range of health benefits. It constitutes a unique symbiotic association, comprising mainly lactic acid bacteria, yeasts, and occasionally acetic acid bacteria, which is strongly influenced by the geographical origin of the grains, the type of milk used, and the manufacture technology applied. Until recently, kefir microbiota has been almost exclusively studied by culture-dependent techniques. However, high-throughput sequencing, alongside omics approaches, has revolutionized the study of food microbial communities. In the present study, the bacterial, and yeast/fungal microbiota of four home-made samples (both grains and drinks), deriving from well spread geographical regions of Greece, and four industrial beverages, was elucidated by culture-dependent and -independent analyses. In all samples, classical microbiological analysis revealed varying populations of LAB and yeasts, ranging from 5.32 to 9.60 log CFU mL–1 or g–1, and 2.49 to 7.80 log CFU mL–1 or g–1, respectively, while in two industrial samples no yeasts were detected. Listeria monocytogenes, Salmonella spp. and Staphylococcus spp. were absent from all the samples analyzed, whereas Enterobacteriaceae were detected in one of them. From a total of 123 isolates, including 91 bacteria and 32 yeasts, Lentilactobacillus kefiri, Leuconostoc mesenteroides, and Lactococcus lactis as well as Kluvyeromyces marxianus and Saccharomyces cerevisiae were the mostly identified bacterial and yeast species, respectively, in the home-made samples. On the contrary, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lacticaseibacillus rhamnosus along with Debaryomyces hansenii and K. marxianus were the main bacterial and yeast species, respectively, isolated from the industrial beverages. In agreement with the identification results obtained from the culture-dependent approaches, amplicon-based metagenomics analysis revealed that the most abundant bacterial genera in almost all home-made samples (both grains and drinks) were Lactobacillus and Lactococcus, while Saccharomyces, Kazachstania, and Kluvyeromyces were the predominant yeasts/fungi. On the other hand, Streptococcus, Lactobacillus, and Lactococcus as well as Kluvyeromyces and Debaryomyces dominated the bacterial and yeast/fungal microbiota, respectively, in the industrial beverages. This is the first report on the microbiota of kefir produced in Greece by a holistic approach combining classical microbiological, molecular, and amplicon-based metagenomics analyses.

Occurrence and dominance of yeast species in naturally fermented milk from the Tibetan Plateau of China

2010 ◽  
Vol 56 (9) ◽  
pp. 707-714 ◽  
Author(s):  
Mei Bai ◽  
Manjun Qing ◽  
Zhuang Guo ◽  
Yong Zhang ◽  
Xia Chen ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Yeast Species ◽  
Debaryomyces Hansenii ◽  
Fermented Milk ◽  
Cow Milk ◽  
The Tibetan Plateau ◽  
Microbiological Analysis ◽  
Sequencing Analysis ◽  
Milk Products ◽  
Fermented Milk Products

To determine which yeasts are present in the naturally fermented milks of China, 69 samples made by the nomads of Tibet were collected from the Tibetan Plateau in China. From these samples, 225 strains of yeast were isolated and identified using conventional microbiological analysis and gene sequencing analysis of the D1/D2 domain of the large subunit (26S) ribosomal DNA. The results showed that the total concentration of yeasts in these samples ranged from 5.01 to 8.97 log10 colony-forming units (CFU)/mL (6.91 ± 1.02 log10 CFU/mL; mean ± SD). The number of cultivable yeasts was higher in the samples from Qinghai (7.55 ± 0.75 log10 CFU/mL) than those from Tibet (6.21 ± 0.79 log10 CFU/mL, P < 0.05). Moreover, there were 15 phylotypes in these 69 samples. Among these phylotypes, Kluyveromyces marxianus (49.3%, frequency percentage), Saccharomyces cerevisiae (62.3%), and Pichia fermentans (46.4%) appeared frequently and can be considered the most common culturable species in naturally fermented milk products. Traditional fermented Mongolian cow milk featured a wide diversity of yeast species, including Issatchenkia orientalis , Kazachstania unisporus , Rhodotorula mucilaginosa , Candida pararugosa , Torulaspora delbrueckii , Geotrichum sp., Kazachstania unisporus , Geotrichum fragrans , Debaryomyces hansenii , Yarrowia lipolytica , Trichosporon gracile , and Pichia membranifaciens . This study provides new data on yeast composition in naturally fermented milk and shows the yeast biodiversity of fermented milk products from the Tibetan Plateau of China.

scholarly journals The symbiotic complex of Dendroctonus simplex: implications in the beetle attack and its life cycle

2019 ◽  
Vol 109 (6) ◽  
pp. 723-732
Author(s):  
A.-A. Durand ◽  
P. Constant ◽  
E. Déziel ◽  
C. Guertin
Keyword(s):  
Defense Mechanisms ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Symbiotic Association ◽  
Forest Pest ◽  
Physiological Processes ◽  
Microbial Assemblage ◽  
Dendroctonus Simplex ◽  
Fungal Microbiota ◽  
Bacteria And Fungi

AbstractThe eastern larch beetle (Dendroctonus simplex Le Conte) is recognized as a serious destructive forest pest in the upper part of North America. Under epidemic conditions, this beetle can attack healthy trees, causing severe damages to larch stands. Dendroctonus species are considered as holobionts, as they engage in multipartite interactions with microorganisms, such as bacteria, filamentous fungi, and yeasts, which are implicated in physiological processes of the insect, such as nutrition. They also play a key role in the beetle's attack, as they are responsible for the detoxification of the subcortical environment and weaken the tree's defense mechanisms. The eastern larch beetle is associated with bacteria and fungi, but their implication in the success of the beetle remains unknown. Here, we investigated the bacterial and fungal microbiota of this beetle pest throughout its ontogeny (pioneer adults, larvae and pupae) by high-throughput sequencing. A successional microbial assemblage was identified throughout the beetle developmental stages, reflecting the beetle's requirements. These results indicate that a symbiotic association between the eastern larch beetle and some of these microorganisms takes place and that this D. simplex symbiotic complex is helping the insect to colonize its host tree and survive the conditions encountered.

scholarly journals Investigation of Physicochemical Indices and Microbial Communities in Termite Fungus-Combs

2021 ◽  
Vol 11 ◽  
Author(s):  
Guiying Yang ◽  
Farhan Ahmad ◽  
Qihuan Zhou ◽  
Meixia Guo ◽  
Shiyou Liang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Inductively Coupled Plasma ◽  
High Performance ◽  
High Throughput Sequencing ◽  
Optical Emission ◽  
Emission Spectrometry ◽  
Symbiotic Association ◽  
Fungus Combs ◽  
16S Rna ◽  
Wide Range

Termitomyces species are wild edible mushrooms that possess high nutritional value and a wide range of medicinal properties. However, the cultivation of these mushrooms is very difficult because of their symbiotic association with termites. In this study, we aimed to examine the differences in physicochemical indices and microbial communities between combs with Termitomyces basidiomes (CF) and combs without Termitomyces basidiomes (CNF). High-performance liquid chromatography (HPLC), inductively coupled plasma optical emission spectrometry (ICP-OES), gas chromatography equipped with a flame ionization detector (GC-FID), some commercial kits, high-throughput sequencing of the 16s RNA, and internal transcribed spacer (ITS) were used. Humidity, pH, and elements, i.e., Al, Ba, Fe, Mn, Ni, S, Ca, and Mg were higher while amino acids particularly alanine, tyrosine, and isoleucine were lower in CF as compared to CNF. The average contents of fatty acids were not significantly different between the two comb categories. The bacterial genera Alistipes, Burkholderia, Sediminibacterium, and Thermus were dominant in all combs. Brevibacterium, Brevundimonas, and Sediminibacterium were significantly more abundant in CF. Basidiomycota and Ascomycota were also identified in combs. Termitomyces clypeatus, Termitomyces sp. Group3, and Termitomyces sp. were the most dominant species in combs. However, any single Termitomyces species was abundantly present in an individual comb.

scholarly journals The symbiotic complex of Dendroctonus simplex: implications in the beetle attack and its life cycle

2018 ◽  
Author(s):  
Audrey-Anne Durand ◽  
Philippe Constant ◽  
Eric Déziel ◽  
Claude Guertin
Keyword(s):  
Defense Mechanisms ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Symbiotic Association ◽  
Forest Pest ◽  
Physiological Processes ◽  
Microbial Assemblage ◽  
Dendroctonus Simplex ◽  
Fungal Microbiota ◽  
Bacteria And Fungi

AbstractThe eastern larch beetle (Dendroctonus simplex Le Conte) is recognized as a serious destructive forest pest in the upper part of North America. Under epidemic conditions, this beetle can attack healthy trees, causing severe damages to larch stands. Dendroctonus species are considered as holobionts, as they engage in multipartite interactions with microorganisms, such as bacteria, filamentous fungi, and yeasts, which are implicated in physiological processes of the insect, such as nutrition. They also play a key role in the beetle’s attack, as they are responsible for the detoxification of the subcortical environment and weaken the tree’s defense mechanisms. The eastern larch beetle is associated with bacteria and fungi, but their implication in the success of the beetle remains unknown. Here, we investigated the bacterial and fungal microbiota of this beetle pest throughout its ontogeny (pioneer adults, larvae and pupae) by high-throughput sequencing. A successional microbial assemblage was identified throughout the beetle developmental stages, reflecting the beetle’s requirements. These results indicate that a symbiotic association between the eastern larch beetle and some of these microorganisms takes place and that this D. simplex symbiotic complex is helping the insect to colonize its host tree and survive the conditions encountered.

scholarly journals Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dieter M. Tourlousse ◽  
Koji Narita ◽  
Takamasa Miura ◽  
Mitsuo Sakamoto ◽  
Akiko Ohashi ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput Sequencing ◽  
Performance Metrics ◽  
Collaborative Study ◽  
Human Microbiome ◽  
Second Phase ◽  
Intermediate Precision ◽  
Fecal Microbiome ◽  
Library Construction ◽  
Wide Range

Abstract Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. Results In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. Conclusions The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products.

scholarly journals Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. 565
Author(s):  
Anindita Lahiri ◽  
Brian R. Murphy ◽  
Trevor R. Hodkinson
Keyword(s):  
Community Composition ◽  
Environmental Effects ◽  
High Throughput Sequencing ◽  
Fungal Community Composition ◽  
Species Identity ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Culture Independent ◽  
The Impact ◽  
Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

scholarly journals The bacterial community of the lone star tick (Amblyomma americanum)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
L. Paulina Maldonado-Ruiz ◽  
Saraswoti Neupane ◽  
Yoonseong Park ◽  
Ludek Zurek
Keyword(s):  
Bacterial Community ◽  
Amblyomma Americanum ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Core Microbiome ◽  
Lone Star Tick ◽  
Animal Pathogens ◽  
Wide Range ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low. Methods We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks. Results We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin. Conclusions No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

Theoretical and practical aspects in determining the current geochemical status of the Crimean peninsula and anthropogenic risk to public health

2021 ◽  
Author(s):  
Elena Evstafeva ◽  
Svetlana Tymchenko ◽  
Anna Bogdanova ◽  
Olga Zalata ◽  
Yuliia Boyarinceva ◽  
...  
Keyword(s):  
Human Body ◽  
Negative Impact ◽  
Chemical Elements ◽  
Ecological Monitoring ◽  
Crimean Peninsula ◽  
Mercury Analysis ◽  
Geographical Regions ◽  
Wide Range ◽  
Biological Substrates ◽  
Cadmium Selenium

&lt;p&gt;The implementation of basic principles of medical and ecological monitoring programs in Crimea previously reported in EGU proceedings consists of determining the content of a wide range of toxic, essential and rare earth elements in various biological substrates: soil, plants, water, human body. Biosubstrates are sampled in different locations with contrast natural and anthropogenic conditions: urbanized-rural, industrial-agricultural, natural resources. Lichens and poplar leaves are used as indicators of environmental contamination, particularly atmospheric pollution; liquid precipitation is used as an indicator showing the negative impact of air pollution on ecosystems; hair is used as an indicator of the total body intake of chemical elements. The update of databases, on some of the territories (Simferopol, Sevastopol, geographical regions with different soil characteristics, etc.) with regard to some of the elements (mercury, lead, cadmium, selenium, etc.) at this stage allowed to determine their biogeochemical status in conditions of intensive growth of anthropogenic load in recent years, and to compare it with the elemental status of the humans living in this territory. The databases for other types of territories continue to be extended, the relationship between morbidity to estimate of the environmental burden of disease for environmentally determined diseases (neurodegenerative, endocrine, respiratory, etc.) and chemical load on the territories, based on USEtox model; the functional state of target systems (nervous, immune, cardiovascular) and level of chemical elements in the human body and the overall elemental imbalance, is established. This has provided us with a degree of understanding on how the degree of population and individual health risk could be determined.&lt;/p&gt;&lt;p&gt;Mercury analysis was funded by RFBR according to the research project &amp;#8470; 18-29-24212\19 entitled &amp;#8220;Development of neutralization of mercury-containing waste without heating and the formation of wastewater&amp;#8221;, 2018&amp;#8211;2021 years; elemental composition was possible to determine due to RFBR project &amp;#8470; 18-45-920042\20 entitled &amp;#8220;Bioecological monitoring of heavy metals at board of Black Sea of Crimea&amp;#8221;, 2018&amp;#8211;2020 years. Physiological part of research was possible to accomplish due to funds by the V.I. Vernadsky Crimean Federal University (Project No VG2019/15, &amp;#1040;&amp;#1040;&amp;#1040;&amp;#1040;-&amp;#1040;20-120012090158-7).&lt;/p&gt;

Rice (Oryza sativa L.) germplasm with better seedling emergence under direct sowing in flooded paddy field

2018 ◽  
Vol 16 (4) ◽  
pp. 352-358 ◽  
Author(s):  
Junichi Kashiwagi ◽  
Koji Hamada ◽  
Yutaka Jitsuyama
Keyword(s):  
Paddy Field ◽  
Oryza Sativa L ◽  
Seedling Emergence ◽  
Screening Method ◽  
Paddy Fields ◽  
Rice Germplasm ◽  
Geographical Regions ◽  
Wide Range ◽  
Cultivation Practice ◽  
Direct Sowing

AbstractDirect sowing of rice in a flooded paddy field is a beneficial cultivation practice for water use and labour efficiency, compared to the transplanted cultivation. However, a drastic reduction in seedling emergence under flooded paddy fields is a serious constraint especially when the seeds fell at deeper soil layers. Suitable rice germplasm for the direct sowing in flooded paddy fields could ensure the success of this cultivation practice. Instead of laborious field-based screening systems, a pot-based screening method was adopted for simplicity and efficient evaluation of seedling emergence of a subset of world rice germplasm (n = 75) at different sowing depths. As a result, two rice genotypes, ‘Vary Futsi’ (landrace from Madagascar, non-glutinous, subspecies Indica) and ‘Dahonggu’ (landrace from China, non-glutinous, subspecies Indica), with consistently better seedling emergence were identified from a wide range of rice germplasm. These genotypes could serve as excellent parents for the breeding program in developing new rice cultivars with the improved seedling emergence in flooded paddy fields. There were no significant differences in the seedling emergence rate in flooded paddy conditions among the groups from various agro-geographical regions.

scholarly journals Improvement Salt Tolerance of Safflower Plants by Endophytic Bacteria

2019 ◽  
Vol 5 ◽  
pp. 38-56 ◽  
Author(s):  
Khulod A. Hemida ◽  
Amany M.M. Reyad
Keyword(s):  
Salt Tolerance ◽  
Plant Growth ◽  
Endophytic Bacteria ◽  
Bacterial Species ◽  
Limiting Factors ◽  
Symbiotic Association ◽  
Bacterial Strains ◽  
Growth Promoters ◽  
Wide Range ◽  
Plant Salt Tolerance

Salinity is one of the most dangerous environmental limiting factors of the plant productivity. A wide range of adaptation strategies is required to overcome salinity stress. However, such strategies seem to be long drawn and cost-intensive. It has been confirmed in recent years that plant growth promoting endophytes (PGPEs) that have the ability to further build a symbiotic association with their host to improve host plant salt tolerance. In our investigation try to improve plant salt tolerance using different species of endophytic bacteria. From the total eight endophytic bacterial species were isolated from root, stem, and leaf of Carthamustinctorius (safflower) plant, two isolates were capable of using 1-aminocyclopropane-1-carboxylic acid (ACC) as a sole nitrogen source, and they are of positive results for (ACC) deaminase activity and indole-3-acetic acid (IAA) production. The bacterial isolates were identified using 16S ribosomal DNA technique as Bacillus cereus and Bacillus aerius and had accession numbers MG708176 and MG711593 respectively, by submitting their sequences in GenBank database. This study showed that the bacterial strains B. cereus and B. aerius are valuable biological plant growth promoters that could enhance salt tolerance in Safflower plants under 100, 200, and 300mMNaCl levels resulting in an increase in plant growth and ascorbate-glutathione redox cycle, in comparison with the non-inoculated controls. Our findings reported that the co-inoculation of the two selected endophytic bacteria strains were successfully isolated from Safflower seedlings significantly alleviated the harmful effects of salt stress, promoted plant growth and biomass yield.

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