scholarly journals Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
S. M. Rafiqul Islam ◽  
Afsana Yeasmin Tanzina ◽  
Md Javed Foysal ◽  
M. Nazmul Hoque ◽  
Meheadi Hasan Rumi ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Its Region ◽  
Total Solid ◽  
Nutritional Composition ◽  
Rrna Gene ◽  
Food Borne ◽  
Nutritional Analysis ◽  
Microbiome Diversity ◽  
Significant Difference ◽  
Nutritional Benefits

AbstractYogurt is one of the most frequently consumed dairy products for nutritional benefits. Although yogurt is enriched with probiotics, it is susceptible to spoilage because of the presence of pathogenic microbes. Spoiled yogurt if consumed can cause food-borne diseases. This study aimed to assess the nutritional composition and microbiome diversity in yogurt manufactured in Bangladesh. Microbial diversity was analyzed through high-throughput sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region. From nutritional analysis, significantly (P < 0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt. Following the classification of Illumina sequences, 84.86% and 72.14% of reads were assigned to bacterial and fungal genera, respectively, with significantly higher taxonomic richness in sour yogurt prepared from buffalo. A significant difference in bacterial (Ppermanova = 0.001) and fungal (Ppermanova = 0.013) diversity between sweet and sour yogurt was recorded. A total of 76 bacterial and 70 fungal genera were detected across these samples which were mostly represented by Firmicutes (92.89%) and Ascomycota (98%) phyla, respectively. This is the first study that accentuates nutritional profiles and microbiome diversity of Bangladeshi yogurt which are crucial in determining both active and passive health effects of yogurt consumption in individuals.

scholarly journals Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh

2021 ◽  
Author(s):  
S. M. Rafiqul Islam ◽  
Afsana Yeasmin Tanzina ◽  
Md Javed Foysal ◽  
M. Nazmul Hoque ◽  
AMAM Z SIDDIKI ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Starter Culture ◽  
Total Solid ◽  
Nutritional Composition ◽  
Taxonomic Richness ◽  
Nutritional Properties ◽  
Safe Production ◽  
Microbiome Diversity ◽  
Significant Difference

Yogurt quality mainly depends on nutritional properties, microbial diversity and purity of starter culture. This study aimed to assess the nutritional composition and microbiome diversity in yogurt. Microbial diversity was analyzed by 16S and 18S rRNA based high-throughput sequencing. Significantly (P<0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt whereas sour varieties had significantly higher ash and minerals. Metagenomic investigation showed that 44.86% and 55.14% reads were assigned to bacterial and fungal taxa, respectively, with significantly higher taxonomic richness in sour yogurt. A significant difference in bacterial (Ppermanova=0.001) and fungal (Ppermanova=0.013) diversity between sweet and sour yogurt was recorded. We detected 76 bacterial and 70 fungal genera across these samples which were mostly represented by Firmicutes (>92%) and Ascomycota (98%) phyla, respectively. Among the detected genera, 36.84% bacterial and 22.86% fungal genera were found in both yogurt types. Our results suggest that Streptococcus (50.82%), Lactobacillus (39.92%), Enterobacter (4.85%), Lactococcus (2.84%) and Aeromonas (0.65%) are the most abundant bacterial genera, while Kluyveromyces (65.75%), Trichosporon (8.21%), Clavispora (7.19%), Candida (6.71%), Iodophanus (2.22%), Apiotrichum (1.94%), and Issatchenkia (1.35%) are the most abundant fungal genera in yogurt metagenomes. This is the first study on nutritional properties and microbiome diversity of Bangladeshi yogurt that would be a benchmark for safe production of quality yogurt by commercial manufacturers.

scholarly journals Comparison of invertebrate diversity in lake waters and their resting eggs in sediments, as revealed by high-throughput sequencing (HTS)

2020 ◽  
pp. 19
Author(s):  
Xiaoyan Wang ◽  
Qing Wang ◽  
Yufeng Yang ◽  
Wenbo Yu
Keyword(s):  
High Throughput ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Essential Feature ◽  
Resting Eggs ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Promising Alternative ◽  
Invertebrate Diversity ◽  
Significant Difference

Aquatic invertebrate diversity reflects water quality and the health of aquatic ecosystems and should be monitored as an essential feature of freshwater ecosystems. The resting eggs of aquatic invertebrates in sediments populate the overlying water. The diversity of invertebrates in waters and their resting eggs in sediments in Baiyangdian Lake, Xiongan, North China, were assessed using high-throughput sequencing (HTS) with a pair of 18S rRNA gene adaptor-linked primers. The total of 99 operational taxonomic units (OTUs) derived from 353,755 invertebrate sequences (mostly zooplankton) were revealed by this study. A total of 50 species in the water samples including 20 rotifers, 11 copepods, 1 cladoceran and 18 other species were sorted out. In the sediment 37 species, including 21 rotifers, 3 copepods, 1 cladoceran and 12 other species, were identified. There were 24 species in common between water and corresponding sediments. Invertebrate OTU richness in water samples was higher than that in sediments (p < 0.01), while there was no significant difference in the Shannon-Wiener index. These results suggest that HTS is a promising alternative for efficient biodiversity assessment and monitoring.

scholarly journals Genotype May Influence Bacterial Diversity in Bark and Bud of Vitis vinifera Cultivars Grown under the Same Environment

2020 ◽  
Vol 10 (23) ◽  
pp. 8405
Author(s):  
Murad Awad ◽  
Georgios Giannopoulos ◽  
Photini V. Mylona ◽  
Alexios N. Polidoros
Keyword(s):  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Molecular Fingerprint ◽  
Microbial Inoculation ◽  
Yield And Quality ◽  
Agronomic Management ◽  
Microbiome Diversity ◽  
Ion Torrent Sequencing ◽  
The Impact

Viticulture is globally an important economic activity, and grapevine microbiomes hold a significant role in influencing yield and quality. Earlier studies showed that cultivar and agronomic management affect grapevine microbiome structure and, potentially, the quality of the end product. While microbial dynamics and ecology were established on some grapevine tissues, i.e., leaves and grapes, there is less knowledge deciphering microbiomes on other tissues, i.e., barks and buds. Moreover, although the impact on the microbiome of the so-called “vitivinicultural terroir” is well established, there are limited data considering microbiomes of genetically diverse cultivars within the same environment. Our study aims to explore microbiome diversity on bud and bark tissues of 37 different grapevine cultivars under the same environment and agronomic management. We targeted the V2-9 regions of the 16S rRNA gene of the microbiomes in bark and buds at the onset of new vegetation and bud expansion using Ion Torrent sequencing technology. Our results show that these tissues display high bacterial diversity regardless of cultivars’ use. Proteobacteria, Bacteroidetes, and Actinobacteria were the most prevalent among 11 detected phyla. The genotype of the cultivar seems to affect bacterial diversity and structure (p < 0.001) within the same environment. Our approach highlights the efficiency of high-throughput sequencing to unfold microbiomes of several grapevine parts that could be an important source of microbial inoculation and an important molecular fingerprint of the wine and grape end products.

scholarly journals Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period

2020 ◽  
Author(s):  
Bridget M Whitney ◽  
Sujatha Srinivasan ◽  
Kenneth Tapia ◽  
Eric Munene Muriuki ◽  
Bhavna H Chohan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Medroxyprogesterone Acetate ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Bacterial Load ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Nugent Score ◽  
Depot Medroxyprogesterone Acetate ◽  
Significant Difference

Abstract Background The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot-medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community. Methods Vaginal swabs were collected from postpartum Kenyan women initiating DMPA-IM or non-hormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S rRNA gene PCR with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to three-months post-initiation were estimated using multivariable linear mixed effects regression. Results Among 54 HIV-negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (Δ=-1.89 (95%CI:-3.53, -0.25; p=0.02) while alpha diversity remained stable (Δ=0.03, 95%CI:-0.24, 0.30; p=0.83). Conversely, Nugent score remained relatively stable among non-HC users (Δ=-0.73, 95%CI:-2.18, 0.73; p=0.33) while alpha diversity decreased (Δ=-0.34, 95%CI:-0.67, -0.001; p=0.05). Total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference=-0.64 log10 gene copies/swab, 95%CI:-1.19, -0.08; p=0.02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different. Conclusions Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.

scholarly journals Global diversity and biogeography of the Zostera marina mycobiome

2020 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Laura E. Vann ◽  
Jonathan A. Eisen
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Zostera Marina ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Marine Fungi ◽  
Its Region ◽  
Global Distribution ◽  
Rrna Gene ◽  
Fungal Community Composition

AbstractSeagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass, Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity, then we tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited, and finally we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. Our results show that the fungal community is significantly different between sites and follows a weak, but significant pattern of distance decay. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome. The Z. marina core leaf and root mycobiomes are dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. and Saccharomyces sp. A few ASVs (e.g. Lobulomyces sp.) appear restricted to one or a handful of locations (e.g. possibly due to local adaptation, deterministic dispersal limitation or seasonal bloom events), while others (e.g. Saccharomyces sp.) are more ubiquitous across all locations suggesting a true global distribution and possible plant-selection. Fungal guilds associated with Z. marina were only weakly identified (10.12% of ITS region and 3.4% 18S rRNA gene ASV guild assignments were considered highly probable) including wood saprotrophs, ectomycorrhizal fungi, endophytic fungi and plant pathogens. Our results are similar to those found for other seagrass species. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that our knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses.

scholarly journals Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

2021 ◽  
Vol 9 (5) ◽  
pp. 1032
Author(s):  
Emily Celeste Fowler ◽  
Prakash Poudel ◽  
Brandon White ◽  
Benoit St-Pierre ◽  
Michael Brown
Keyword(s):  
Striped Bass ◽  
Soybean Meal ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Hybrid Striped Bass ◽  
Bacterial Composition ◽  
Morone Chrysops ◽  
Fish Diets ◽  
Significant Difference

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

scholarly journals “Comparative Analysis of Gut Microbiome in Individuals of the Old Civilization of Caral-Supe Based on Data from 16S rRNA and ITS region”

2020 ◽  
Author(s):  
Andrés Vásquez-Domínguez ◽  
Luis Jaramillo-Valverde ◽  
Kelly S. Levano ◽  
Pedro Novoa-Bellota ◽  
Marco Machaguay-Romero ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Ancient Civilization ◽  
High Throughput Sequencing Data

ABSTRACTGenetic and microbiome studies of ancient Caral-Supe civilization have not yet been published. For this reason, the objective of this work is to identify the microorganisms and possible diseases that existed in this ancient civilization using coprolites samples. To do this, two coprolites samples were analyzing through high-throughput sequencing data of 16S rRNA gene and an intergenic region (ITS).

scholarly journals Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6684 ◽  
Author(s):  
Siyu Han ◽  
Yu Guan ◽  
Hailong Dou ◽  
Haitao Yang ◽  
Meng Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Invasive Approach ◽  
Fecal Samples ◽  
Significant Difference

The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.

scholarly journals Alterations and Correlations in Microbial Community and Metabolome Characteristics in Generalized Aggressive Periodontitis

2020 ◽  
Vol 11 ◽  
Author(s):  
Meng Shi ◽  
Yiping Wei ◽  
Yong Nie ◽  
Cui Wang ◽  
Fei Sun ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Gingival Crevicular Fluid ◽  
Enrichment Analysis ◽  
Aggressive Periodontitis ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Metabolic Profiles ◽  
Galactose Metabolism ◽  
Significant Difference

This study aimed to characterize the microbial community and metabolic profiles in generalized aggressive periodontitis (AgP) using 16S ribosomal RNA (rRNA) gene high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS). A total of 146 subgingival plaque samples and 50 gingival crevicular fluid (GCF) samples were collected from 24 patients with AgP and 10 periodontally healthy subjects (PH). Striking differences were observed in subgingival microbiome and GCF metabolomics between patients with AgP and PH, but not between samples with different probing depths (PDs). Metabolomics analysis combined with enrichment analysis showed that periodontitis significantly altered the concentration of compounds associated with biosynthesis of amino acids (e.g., alanine, leucine, isoleucine, and valine), galactose metabolism (e.g., myo-inositol, galactose, glucose, and hexitol), and pyrimidine metabolism (e.g., uracil, uridine, beta alanine, and thymine). Correlation analysis showed that the genera with significant difference between AgP and PH were usually significantly correlated with more metabolites, such as Aggregatibacter, Rothia, Peptostreptococcaceae_[XI][G-5], and Bacteroidaceae_[G-1]. While glucose and oxoproline had the most significant correlations with microorganisms. Our results revealed distinct microbial communities and metabolic profiles between AgP and PH. The significant correlation between microbial taxa and metabolites suggested the possible mechanisms for periodontitis. Our results also provided effective approaches for detecting periodontal disease and managing periodontitis.

scholarly journals Unique Microbial Phylotypes in Namib Desert Dune and Gravel Plain Fairy Circle Soils

2016 ◽  
Vol 82 (15) ◽  
pp. 4592-4601 ◽  
Author(s):  
Andries J. van der Walt, ◽  
Riegardt M. Johnson ◽  
Don A. Cowan ◽  
Mary Seely ◽  
Jean-Baptiste Ramond
Keyword(s):  
Microbial Communities ◽  
Internal Transcribed Spacer ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Soil Samples ◽  
Grass Species ◽  
Rrna Gene ◽  
Namib Desert ◽  
Phytopathogenic Microorganisms ◽  
And Control

ABSTRACTFairy circles (FCs) are barren circular patches of soil surrounded by grass species. Their origin is poorly understood. FCs feature in both the gravel plains and the dune fields of the Namib Desert. While a substantial number of hypotheses to explain the origin and/or maintenance of fairy circles have been presented, none are completely consistent with either their properties or their distribution. In this study, we investigated the hypothesis that FC formation in dunes and gravel plains is due to microbial phytopathogenesis. Surface soils from five gravel plain and five dune FCs, together with control soil samples, were analyzed using high-throughput sequencing of bacterial/archaeal (16S rRNA gene) and fungal (internal transcribed spacer [ITS] region) phylogenetic markers. Our analyses showed that gravel plain and dune FC microbial communities are phylogenetically distinct and that FC communities differ from those of adjacent vegetated soils. Furthermore, various soil physicochemical properties, particularly the pH, the Ca, P, Na, and SO4contents, the soil particle size, and the percentage of carbon, significantly influenced the compositions of dune and gravel plain FC microbial communities, but none were found to segregate FC and vegetated soil communities. Nevertheless, 9 bacterial, 1 archaeal, and 57 fungal phylotypes were identified as FC specific, since they were present within the gravel plain and dune FC soils only, not in the vegetated soils. Some of these FC-specific phylotypes were assigned to taxa known to harbor phytopathogenic microorganisms. This suggests that these FC-specific microbial taxa may be involved in the formation and/or maintenance of Namib Desert FCs.IMPORTANCEFairy circles (FCs) are mysterious barren circular patches of soil found within a grass matrix in the dune fields and gravel plains of the Namib Desert. Various hypotheses attempting to explain this phenomenon have been proposed. To date, however, none have been successful in fully explaining the etiology of FCs, particularly since gravel plain FCs have been largely ignored. In this study, we investigated the hypothesis that microorganisms could be involved in the FC phenomenon through phytopathogenesis. We show that the microbial communities in FC and control vegetated soil samples were significantly different. Furthermore, we detected 67 FC-specific microbial phylotypes, i.e., phylotypes present solely in both gravel plain and dune FC soils, some of which were closely related to known phytopathogens. Our results, therefore, demonstrate that microorganisms may play a role in the formation and/or maintenance of Namib Desert FCs, possibly via phytopathogenic activities.

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