scholarly journals Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds

2019 ◽  
Vol 65 (9) ◽  
pp. 668-680
Author(s):  
Asma Jaba ◽  
Fadi Dagher ◽  
Amir Mehdi Hamidi Oskouei ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Relative Abundance ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Physiological Traits ◽  
Theoretical Frameworks ◽  
Community Assemblage ◽  
Microbial Species ◽  
Cultivable Bacteria ◽  
Occurrence Patterns

Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.

scholarly journals Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Florencia A. Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Bacterial Concentrations

ABSTRACT Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentrations of individual bacterial species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We sought to determine the accuracy of an inferred measure of bacterial concentration using total bacterial load and relative abundance. We analyzed 1,320 samples from 20 women with a history of frequent bacterial vaginosis who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, P < 2.2e–16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacteria associated with larger errors. A total of 92% of the >0.5-log10 errors occurred when the relative abundance was <10%. Many errors occurred during early bacterial expansion from or late contraction to low abundance. When the relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome. However, targeted qPCR is required to capture bacteria at low relative abundance and is preferable for characterizing growth and decay kinetics of single species. IMPORTANCE Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species’ relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species’ concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

scholarly journals Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome

2019 ◽  
Author(s):  
Florencia Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Associated Bacteria

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.

scholarly journals Sex-Based Diverse Plaque Microbiota in Children with Severe Caries

2020 ◽  
Vol 99 (6) ◽  
pp. 703-712 ◽  
Author(s):  
V.C. de Jesus ◽  
R. Shikder ◽  
D. Oryniak ◽  
K. Mann ◽  
A. Alamri ◽  
...  
Keyword(s):  
Young Children ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Assessment Tools ◽  
Rrna Gene ◽  
Male And Female ◽  
Significant Difference ◽  
Female Children ◽  
Related Quality

Severe early childhood caries (S-ECC) is a multifactorial disease that can lead to suffering and reduced oral health–related quality of life in young children. The bacterial and fungal composition of dental plaque and how children’s sex is associated with S-ECC are largely unknown. In this study, V4-16S rRNA and ITS1 rRNA gene amplicon sequencing was used to compare the plaque bacteriome and mycobiome of children <72 mo of age: 40 with S-ECC (15 males, 25 females) and 40 caries-free (19 males, 21 females). Health- and nutrition-related questionnaire data were also investigated. This study aimed to analyze potential sex-based differences in the supragingival plaque microbiota of young children with S-ECC and those caries-free. Behavioral and nutritional habit differences were observed between children with S-ECC and those caries-free and between male and female children. Overall, higher levels of Veillonella dispar, Streptococcus mutans, and other bacterial species were found in the S-ECC group as compared with caries-free controls ( P < 0.05). A significant difference in the abundance of Neisseria was observed between males and females with S-ECC ( P < .05). Fungal taxonomic analysis showed significantly higher levels of Candida dubliniensis in the plaque of children with S-ECC as compared with those caries-free ( P < 0.05), but no differences were observed with Candida albicans ( P > 0.05). Significant differences in the relative abundance of Mycosphaerella, Cyberlindnera, and Trichosporon fungal species were also observed between the caries-free and S-ECC groups ( P < 0.05). Machine learning analysis revealed the most important bacterial and fungal species for classifying S-ECC versus caries-free. Different patterns of crosstalk between microbial species were observed between male and female children. Our work demonstrates that plaque microbiota and sex may be important determinants for S-ECC and could be factors to consider for inclusion in caries risk assessment tools.

scholarly journals Temporal Microbial Community Dynamics Within a Unique Acid Saline Lake

2021 ◽  
Vol 12 ◽  
Author(s):  
Noor-Ul-Huda Ghori ◽  
Michael J. Wise ◽  
Andrew S. Whiteley
Keyword(s):  
Microbial Community ◽  
Environmental Conditions ◽  
Fungal Diversity ◽  
Community Dynamics ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Hypersaline Lake ◽  
Microbial Community Dynamics ◽  
Abundance And Diversity

Lake Magic is an extremely acidic, hypersaline lake found in Western Australia, with the highest concentrations of aluminum and silica in the world. Previous studies of Lake Magic diversity have revealed that the lake hosts acid- and halotolerant bacterial and fungal species. However, they have not canvassed microbial population dynamics across flooding, evapo-concentration and desiccation stages. In this study, we used amplicon sequencing and potential function prediction on sediment and salt mat samples. We observed that the bacterial and fungal diversity in Lake Magic is strongly driven by carbon, temperature, pH and salt concentrations at the different stages of the lake. We also saw that the fungal diversity decreased as the environmental conditions became more extreme. However, prokaryotic diversity was very dynamic and bacteria dominated archaeal species, both in abundance and diversity, perhaps because bacteria better tolerate the extreme variation in conditions. Bacterial species diversity was the highest during early flooding stage and decreased during more stressful conditions. We observed an increase in acid tolerant and halotolerant species in the sediment, involved in functions such as sulfur and iron metabolism, i.e., species involved in buffering the external environment. Thus, due to activity within the microbial community, the environmental conditions in the sediment do not change to the same degree as conditions in the salt mat, resulting in the sediment becoming a safe haven for microbes, which are able to thrive during the extreme conditions of the evapo-concentration and desiccation stages.

scholarly journals Investigation of co-ensiling for the storage of grain stillage and Jerusalem artichoke residue from inulin extraction

BioResources ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. 7300-7336
Author(s):  
Haiwei Ren ◽  
Li Wang ◽  
Mei Li ◽  
Yuchun Zhang ◽  
Zhiye Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Species ◽  
Jerusalem Artichoke ◽  
Fungal Species ◽  
Middle Level ◽  
Water Soluble ◽  
Soluble Carbohydrate ◽  
Mixing Ratios ◽  
Feed Value ◽  
Water Soluble Carbohydrate

Jerusalem artichoke residue (JR) was co-ensiled with grain stillage (GS) at various weight mixing ratios (JR only, 4 to 1, 2 to 1, 1.2 to 1, 1 to 1.5, 1 to 2.7, 1 to 7, and GS only) for 10, 30, and 60 d for agricultural biomass storage. Results showed that the middle level of GS to JR ratios, e.g., 1.2 to 1 and 1 to 1.5, achieved the best co-ensiling performance among all studied ratios. The water-soluble carbohydrate (WSC) contents were significantly higher than those of the other treatments (p < 0.05), and the lignocellulose contents were significantly lower than those of other treatments (p < 0.05). The silages ensiled at the above-mentioned ratios had a higher feed value and biodegradation potential than other ratios. Lactobacillus was the dominant bacterial species during the ensiling process, and its relative abundance was significantly correlated with the content of different components, e.g., WSC, crude protein, and starch, as well as fermentation characteristics. Fungal species, e.g., Kluyveromyces and Monascus were also observed, and the relative abundance of which was positively correlated with different nutritional components. In conclusion, GS and JR can be successfully stored via co-ensiling.

scholarly journals Comparative analysis of the rhizosphere and endophytic microbiomes across apple rootstock genotypes in replant orchard soils

2021 ◽  
Author(s):  
Christopher Van Horn ◽  
Tracey Somera ◽  
Mark Mazzola
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Management Practices ◽  
Arbuscular Mycorrhizal ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Apple Rootstock ◽  
Apple Rootstocks ◽  
Apple Replant Disease ◽  
Taxonomic Range

Apple replant disease (ARD), caused by a complex of soil-borne pathogens, negatively impacts tree health and productivity in new orchard plantings at sites previously planted to apple. Use of new disease tolerant apple rootstock genotypes may diminish growth limiting effects of ARD, however the influence of rootstock genotype on modulating the rhizosphere and endophytic microbiome to enable ARD tolerance is not fully understood. Composition of the rhizosphere and root endophytic microbiomes was characterized across a diversity of apple rootstock genotypes. A series of tolerant (G.210, G.41, G.890, and G.935) and susceptible (M.26 and M.9) rootstock cultivars were consecutively planted into orchard replant soil containing a known pathogen complex. Amplicon sequencing was used to determine simultaneously the presence of a broad taxonomic range of organisms and their relative abundance. Microbial communities exhibited significant differences in composition between the rhizosphere and endophytic environments in terms of species diversity, content, and abundance. Significant differences in composition of the endophytic and rhizosphere microbiomes were observed between rootstock genotypes. Among rootstock endophytic fungal communities, rootstock G.890 samples consistently harbored the highest percentage of arbuscular mycorrhizal fungal species (>5% of total). Ilyonectria spp., which may function as a pathogen of apple, were detected at high relative abundance in the endosphere of all genotypes, with the highest relative abundance in M.26. These results provide further insight into rhizosphere and endophytic microbial communities of apple rootstocks, which could be exploited or manipulated to improve tree fruit agricultural management practices with respect to plant nutrition and disease control.

Substituted 6,7-dimethoxy-5-oxo-2,3,5,9b-tetrahydrothiazolo[2,3-a]isoindole- 3-1,1-dioxide Derivatives with Antimicrobial Activity and Docking Assisted Prediction of the Mechanism of their Antibacterial and Antifungal Properties

2020 ◽  
Vol 20 (29) ◽  
pp. 2681-2691
Author(s):  
Athina Geronikaki ◽  
Victor Kartsev ◽  
Phaedra Eleftheriou ◽  
Anthi Petrou ◽  
Jasmina Glamočlija ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Antifungal Activity ◽  
Drug Targets ◽  
Bacterial Species ◽  
Pharmaceutical Research ◽  
Docking Studies ◽  
Fungal Species ◽  
Docking Analysis ◽  
E Coli ◽  
Antibacterial And Antifungal

Background: Although a great number of the targets of antimicrobial therapy have been achieved, it remains among the first fields of pharmaceutical research, mainly because of the development of resistant strains. Docking analysis may be an important tool in the research for the development of more effective agents against specific drug targets or multi-target agents 1-3. Methods: In the present study, based on docking analysis, ten tetrahydrothiazolo[2,3-a]isoindole derivatives were chosen for the evaluation of the antimicrobial activity. Results: All compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species being, in some cases, more potent than ampicillin and streptomycin against all species. The most sensitive bacteria appeared to be S. aureus and En. Cloacae, while M. flavus, E. coli and P. aeruginosa were the most resistant ones. The compounds were also tested for their antifungal activity against eight fungal species. All compounds exhibited good antifungal activity better than reference drugs bifonazole (1.4 – 41 folds) and ketoconazole (1.1 – 406 folds) against all fungal species. In order to elucidate the mechanism of action, docking studies on different antimicrobial targets were performed. Conclusion: According to docking analysis, the antifungal activity can be explained by the inhibition of the CYP51 enzyme for most compounds with a better correlation of the results obtained for the P.v.c. strain (linear regression between estimated binding Energy and log(1/MIC) with R 2 =0.867 and p=0.000091 or R 2 = 0.924, p= 0.000036, when compound 3 is excluded.

scholarly journals Microbial Communities, Metabolites, Fermentation Quality and Aerobic Stability of Whole-Plant Corn Silage Collected from Family Farms in Desert Steppe of North China

Processes ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 784
Author(s):  
Chao Wang ◽  
Lin Sun ◽  
Haiwen Xu ◽  
Na Na ◽  
Guomei Yin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Fungal Diversity ◽  
North China ◽  
Bacterial Species ◽  
Fungal Species ◽  
Family Farms ◽  
Aerobic Stability ◽  
Whole Plant ◽  
Lactobacillus Kefiri

Whole-plant corn silages on family farms were sampled in Erdos (S1), Baotou (S2), Ulanqab (S3), and Hohhot (S4) in North China, after 300 d of ensiling. The microbial communities, metabolites, and aerobic stability were assessed. Lactobacillusbuchneri, Acinetobacter johnsonii, and unclassified Novosphingobium were present at greater abundances than others in S2 with greater bacterial diversity and metabolites. Lactobacillus buchneri, Lactobacillus parafarraginis, Lactobacillus kefiri, and unclassified Lactobacillus accounted for 84.5%, and 88.2%, and 98.3% of bacteria in S1, S3, and S4, respectively. The aerobic stability and fungal diversity were greater in S1 and S4 with greater abundances of unclassified Kazachstania, Kazachstania bulderi, Candida xylopsoci, unclassified Cladosporium, Rhizopus microspores, and Candida glabrata than other fungi. The abundances of unclassified Kazachstania in S2 and K. bulderi in S3 were 96.2% and 93.6%, respectively. The main bacterial species in S2 were L. buchneri, A. johnsonii, and unclassified Novosphingobium; Lactobacillus sp. dominated bacterial communities in S1, S3, and S4. The main fungal species in S1 and S4 were unclassified Kazachstania, K. bulderi, C. xylopsoci, unclassified Cladosporium, R. microspores, and C. glabrata; Kazachstania sp. dominated fungal communities in S2 and S3. The high bacterial diversity aided the accumulation of metabolites, and the broad fungal diversity improved the aerobic stability.

scholarly journals Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lito E. Papanicolas ◽  
Sarah K. Sims ◽  
Steven L. Taylor ◽  
Sophie J. Miller ◽  
Christos S. Karapetis ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Haematological Malignancy ◽  
Amplicon Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Conventional Chemotherapy ◽  
Myelosuppressive Chemotherapy ◽  
Gram Positive Bacteria ◽  
Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

scholarly journals Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 482
Author(s):  
Jae-Kwon Jo ◽  
Seung-Ho Seo ◽  
Seong-Eun Park ◽  
Hyun-Woo Kim ◽  
Eun-Ju Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
High Fat Diet ◽  
Amplicon Sequencing ◽  
Gas Chromatography Mass Spectrometry ◽  
Control Group ◽  
Rrna Gene ◽  
High Fat ◽  
Underlying Mechanisms ◽  
Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

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