Contribution of Microorganisms to Biogenic Amine Accumulation during Fish Sauce Fermentation and Screening of Novel Starters

In this study, high-throughput sequencing and culture-dependent and HPLC methods were used to investigate the contribution and regulation of biogenic amines (BAs) by dominant microorganisms during fish sauce fermentation. The results showed that the microbial composition constantly changed with the fermentation of fish sauce. Tetragenococcus (40.65%), Lentibacillus (9.23%), Vagococcus (2.20%), Psychrobacter (1.80%), Pseudomonas (0.98%), Halomonas (0.94%) and Staphylococcus (0.16%) were the dominant microflora in fish sauce. The content of BAs gradually increased as the fermentation progressed. After 12 months of fermentation, the histamine content (55.59 mg/kg) exceeded the toxic dose recommended by the Food and Drug Administration (FDA). Correlation analysis showed that dominant microorganisms have a great contribution to the accumulation of BAs. By analyzing the BA production capacity of dominant isolates, the accumulation of BAs in fish sauce might be promoted by Tetragenococcus and Halomonas. Moreover, four strains with high BA reduction ability were screened out of 44 low BA-producing dominant strains, and their influence on BA accumulation in fermented foods was determined. Results demonstrated that Staphylococcus nepalensis 5-5 and Staphylococcus xylosus JCM 2418 might be the potential starters for BA control. The present study provided a new idea for the control of BAs in fermented foods.

Download Full-text

Microbiota identified from preserved Anopheles

Malaria Journal ◽

10.1186/s12936-021-03754-7 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Bianca E Silva ◽

Zvifadzo Matsena Zingoni ◽

Lizette L. Koekemoer ◽

Yael L. Dahan-Moss

Keyword(s):

Microbial Diversity ◽

Vector Competence ◽

Mosquito Species ◽

Anopheles Funestus ◽

Cost Effective ◽

Diversity Indices ◽

Malaria Vectors ◽

Microbial Composition ◽

Culture Independent ◽

Culture Dependent

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

Download Full-text

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

Journal of Fungi ◽

10.3390/jof7070565 ◽

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.

Download Full-text

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

Download Full-text

Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽

10.1186/s12915-021-01003-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Timothy P. Jenkins ◽

David I. Pritchard ◽

Radu Tanasescu ◽

Gary Telford ◽

Marina Papaiakovou ◽

...

Keyword(s):

Multiple Sclerosis ◽

Experimental Infection ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Placebo Treatment ◽

Sequencing Data ◽

Faecal Microbiota ◽

Microbial Composition ◽

Necator Americanus ◽

Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

Download Full-text

Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

F1000Research ◽

10.12688/f1000research.8986.1 ◽

2016 ◽

Vol 5 ◽

pp. 1492 ◽

Cited By ~ 148

Author(s):

Ben J. Callahan ◽

Kris Sankaran ◽

Julia A. Fukuyama ◽

Paul J. McMurdie ◽

Susan P. Holmes

Keyword(s):

High Throughput Sequencing ◽

Linear Models ◽

Reference Database ◽

Rrna Gene ◽

Microbial Composition ◽

Nonparametric Testing ◽

Abundance Estimates ◽

Taxonomic Markers ◽

Microbiome Data ◽

Microbiome Data Analysis

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

Download Full-text

Altered Fecal Metabolites and Colonic Glycerophospholipids Were Associated With Abnormal Composition of Gut Microbiota in a Depression Model of Mice

Frontiers in Neuroscience ◽

10.3389/fnins.2021.701355 ◽

2021 ◽

Vol 15 ◽

Author(s):

Xue Gong ◽

Cheng Huang ◽

Xun Yang ◽

Jianjun Chen ◽

Juncai Pu ◽

...

Keyword(s):

Correlation Analysis ◽

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Underlying Mechanism ◽

Rrna Gene ◽

Mice Model ◽

Microbial Composition ◽

Gas And Liquid Chromatography ◽

Correlation Analysis Method ◽

Rrna Gene Sequencing

The microbiota–gut–brain axis has been considered to play an important role in the development of depression, but the underlying mechanism remains unclear. The gastrointestinal tract is home to trillions of microbiota and the colon is considered an important site for the interaction between microbiota and host, but few studies have been conducted to evaluate the alterations in the colon. Accordingly, in this study, we established a chronic social defeated stress (CSDS) mice model of depression. We applied 16S rRNA gene sequencing to assess the gut microbial composition and gas and liquid chromatography–mass spectroscopy to identify fecal metabolites and colonic lipids, respectively. Meanwhile, we used Spearman’s correlation analysis method to evaluate the associations between the gut microbiota, fecal metabolites, colonic lipids, and behavioral index. In total, there were 20 bacterial taxa and 18 bacterial taxa significantly increased and decreased, respectively, in the CSDS mice. Further, microbial functional prediction demonstrated a disturbance of lipid, carbohydrate, and amino acid metabolism in the CSDS mice. We also found 20 differential fecal metabolites and 36 differential colonic lipids (in the category of glycerolipids, glycerophospholipids, and sphingolipids) in the CSDS mice. Moreover, correlation analysis showed that fecal metabolomic signature was associated with the alterations in the gut microbiota composition and colonic lipidomic profile. Of note, three lipids [PC(16:0/20:4), PG(22:6/22:6), and PI(18:0/20:3), all in the category of glycerophospholipids] were significantly associated with anxiety- and depression-like phenotypes in mice. Taken together, our results indicated that the gut microbiota might be involved in the pathogenesis of depression via influencing fecal metabolites and colonic glycerophospholipid metabolism.

Download Full-text

Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches

10.21203/rs.3.rs-28393/v1 ◽

2020 ◽

Author(s):

Chuanbo Zhang ◽

Chao-Hui Ren ◽

Yan-Li Wang ◽

Qi-Qi Wang ◽

Yun-Sheng Wang ◽

...

Keyword(s):

Community Structure ◽

High Throughput ◽

Fungal Community ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Bioactive Metabolites ◽

Fungal Community Structure ◽

Ophiocordyceps Sinensis ◽

Culturable Fungi ◽

Culture Dependent

Abstract Background The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approach. Results A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices (EMC), Ophiocordyceps, Sebacinia, Archaeorhizomyces were predominant genera with the abundance of 95.86%, 1.14%, 0.85%, respectively. Total 66 genera were identified from soil microhabitat, Inocybe, Archaeorhizomyces, Unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, Unclassified Ascomycota, Unclassified Fungi were predominant genera with an average abundance of 53.32%, 8.69%, 8.12%, 8.12%, 7.21%, 4.6%, 3.08% and 3.05%, respectively. The fungal communities in external mycelial cortices (EMC) were significantly distinct from the soil microhabitat (Soil). Meanwhile, seven culture media that benefit for the growth of O. sinensis were used to isolate culturable fungi at 16 °C, resulted in 77 fungal strains isolated for rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora, Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera of total isolates. Conclusions The significantly distinction and overlap in fungal community structure between two approaches highlight that integration of approaches would generate more information than either of them. Our finding is the first investigation of fungal community structure of natural O. sinensis by two approachs, provide new insight into O. sinensis associated fungi, and support that microbiota of O. sinensis is an untapped source for novel bioactive metabolites discovery.

Download Full-text

Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter

Microorganisms ◽

10.3390/microorganisms8070982 ◽

2020 ◽

Vol 8 (7) ◽

pp. 982

Author(s):

Lucas von Gastrow ◽

Marie-Noëlle Madec ◽

Victoria Chuat ◽

Stanislas Lubac ◽

Clémence Morinière ◽

...

Keyword(s):

Microbial Community ◽

Fermentation Process ◽

Fermented Milk ◽

Geotrichum Candidum ◽

Microbial Composition ◽

Streptococcus Species ◽

Culture Independent ◽

History Of ◽

Points Of View ◽

Culture Dependent

Gwell is a traditional mesophilic fermented milk from the Brittany region of France. The fermentation process is based on a back-slopping method. The starter is made from a portion of the previous Gwell production, so that Gwell is both the starter and final product for consumption. In a participatory research framework involving 13 producers, Gwell was characterized from both the sensory and microbial points of view and was defined by its tangy taste and smooth and dense texture. The microbial community of typical Gwell samples was studied using both culture-dependent and culture-independent approaches. Lactococcus lactis was systematically identified in Gwell, being represented by both subspecies cremoris and lactis biovar diacetylactis which were always associated. Geotrichum candidum was also found in all the samples. The microbial composition was confirmed by 16S and ITS2 metabarcoding analysis. We were able to reconstruct the history of Gwell exchanges between producers, and thus obtained the genealogy of the samples we analyzed. The samples clustered in two groups which were also differentiated by their microbial composition, and notably by the presence or absence of yeasts identified as Kazachstania servazii and Streptococcus species.

Download Full-text

Bioregional Alterations in Gut Microbiome Contribute to the Plasma Metabolomic Changes in Pigs Fed with Inulin

Microorganisms ◽

10.3390/microorganisms8010111 ◽

2020 ◽

Vol 8 (1) ◽

pp. 111 ◽

Cited By ~ 5

Author(s):

Weida Wu ◽

Li Zhang ◽

Bing Xia ◽

Shanlong Tang ◽

Lei Liu ◽

...

Keyword(s):

Gut Microbiota ◽

High Throughput Sequencing ◽

Mantel Test ◽

Plasma Metabolites ◽

Microbial Composition ◽

Regional Effects ◽

Host Interaction ◽

Β Diversity ◽

Branched Chain ◽

Host Metabolism

Inulin (INU) is a non-digestible carbohydrate, known for its beneficial properties in metabolic disorders. However, whether and how gut microbiota in its regulation contributes to host metabolism has yet to be investigated. We conduct this study to examine the possible associations between the gut microbiota and circulating gut microbiota–host co-metabolites induced by inulin interventions. Plasma and intestinal site samples were collected from the pigs that have consumed inulin diet for 60 days. High-throughput sequencing was adopted for microbial composition, and the GC-TOF-MS-based metabolomics were used to characterize featured plasma metabolites upon inulin intervention. Integrated multi-omics analyses were carried out to establish microbiota–host interaction. Inulin consumption decreased the total cholesterol (p = 0.04) and glucose (p = 0.03) level in serum. Greater β-diversity was observed in the cecum and colon of inulin-fed versus that of control-fed pigs (p < 0.05). No differences were observed in the ileum. In the cecum, 18 genera were altered by inulin, followed by 17 in the colon and 6 in the ileum. Inulin increased propionate, and isobutyrate concentrations but decreased the ratio of acetate to propionate in the cecum, and increased total short fatty acids, valerate, and isobutyrate concentrations in the colon. Metabolomic analysis reveals that indole-3-propionic acid (IPA) was significantly higher, and the branched-chain amino acids (BCAA), L-valine, L-isoleucine, and L-leucine are significantly lower in the inulin groups. Mantel test and integrative analysis revealed associations between plasma metabolites (e.g., IPA, BCAA, L-tryptophan) and inulin-responsive cecal microbial genera. These results indicate that the inulin has regional effects on the intestine microbiome in pigs, with the most pronounced effects occurring in the cecum. Moreover, cecum microbiota plays a pivotal role in the modulation of circulating host metabolites upon inulin intervention

Download Full-text

Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16010001 ◽

2018 ◽

Vol 16 (1) ◽

pp. 1 ◽

Cited By ~ 14

Author(s):

Yong Li ◽

Jianqiang Zhang ◽

Zhiliang Gong ◽

Wenlai Xu ◽

Zishen Mou

Keyword(s):

Correlation Analysis ◽

High Throughput Sequencing ◽

Gene Diversity ◽

Pearson Correlation ◽

Glucose Dehydrogenase ◽

Sampling Site ◽

Soluble Phosphate ◽

High Genetic Diversity ◽

Alpha And Beta Diversity ◽

Insoluble Phosphate

Quinoprotein glucose dehydrogenase (GDH) is the most important enzyme of inorganic phosphorus-dissolving metabolism, catalyzing the oxidation of glucose to gluconic acid. The insoluble phosphate in the sediment is converted into soluble phosphate, facilitating mass reproduction of algae. Therefore, studying the diversity of gcd genes which encode GDH is beneficial to reveal the microbial group that has a significant influence on the eutrophication of water. Taking the eutrophic Sancha Lake sediments as the research object, we acquired samples from six sites in the spring and autumn. A total of 219,778 high-quality sequences were obtained by DNA extraction of microbial groups in sediments, PCR amplification of the gcd gene, and high-throughput sequencing. Six phyla, nine classes, 15 orders, 29 families, 46 genera, and 610 operational taxonomic units (OTUs) were determined, suggesting the high genetic diversity of gcd. Gcd genes came mainly from the genera of Rhizobium (1.63–77.99%), Ensifer (0.13–56.95%), Shinella (0.32–25.49%), and Sinorhizobium (0.16–11.88%) in the phylum of Proteobacteria (25.10–98.85%). The abundance of these dominant gcd-harboring bacteria was higher in the spring than in autumn, suggesting that they have an important effect on the eutrophication of the Sancha Lake. The alpha and beta diversity of gcd genes presented spatial and temporal differences due to different sampling site types and sampling seasons. Pearson correlation analysis and canonical correlation analysis (CCA) showed that the diversity and abundance of gcd genes were significantly correlated with environmental factors such as dissolved oxygen (DO), phosphorus hydrochloride (HCl–P), and dissolved total phosphorus (DTP). OTU composition was significantly correlated with DO, total organic carbon (TOC), and DTP. GDH encoded by gcd genes transformed insoluble phosphate into dissolved phosphate, resulting in the eutrophication of Sancha Lake. The results suggest that gcd genes encoding GDH may play an important role in lake eutrophication.

Download Full-text