scholarly journals Metagenomic analysis reveals rapid development of soil biota on fresh volcanic ash

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hokyung Song ◽  
Dorsaf Kerfahi ◽  
Koichi Takahashi ◽  
Sophie L. Nixon ◽  
Binu M. Tripathi ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Volcanic Ash ◽  
Rapid Development ◽  
Soil Biota ◽  
Rrna Gene ◽  
Natural Ecosystems ◽  
Soil Community ◽  
Range Of Functions ◽  
Similar Range ◽  
Metagenome Sequencing

AbstractLittle is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates across Japan and compared over 3 years, against the developed soils of surrounding natural ecosystems. DNA was extracted from mesocosms and community composition assessed using 16S rRNA gene sequences. Metagenome sequences were obtained using shotgun metagenome sequencing. While at 12 months there was insufficient DNA for sequencing, by 24 months and 36 months, the ash-soil metagenomes already showed a similar diversity of functional genes to the developed soils, with a similar range of functions. In a surprising contrast with our hypotheses, we found that the developing ash-soil community already showed a similar gene function diversity, phylum diversity and overall relative abundances of kingdoms of life when compared to developed forest soils. The ash mesocosms also did not show any increased relative abundance of genes associated with autotrophy (rbc, coxL), nor increased relative abundance of genes that are associated with acquisition of nutrients from abiotic sources (nifH). Although gene identities and taxonomic affinities in the developing ash-soils are to some extent distinct from the natural vegetation soils, it is surprising that so many of the key components of a soil community develop already by the 24-month stage. In this system, however, rapid development may be facilitated by the relatively moderate pH of the Sakurajima ash, proximity of our mesocosms to propagule sources, and the rapid establishment of a productive bryophyte and lichen layer on the surface. Ash from other volcanoes richer in acids or more distant from propagule sources could show a different pattern and slower soil biota development.

scholarly journals Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health

2020 ◽  
Author(s):  
Roland Wirth ◽  
Gergely Maróti ◽  
Lídia Lipták ◽  
Mónika Mester ◽  
Alaa Al Ayoubi ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Amplicon Sequencing ◽  
Diagnostic Value ◽  
Orthodontic Appliances ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Abundance Pattern ◽  
Gingival Health ◽  
Characteristic Features ◽  
Metagenome Sequencing

Abstract Background: Comparison of the microbiomes in supragingival biofilm and saliva samples collected from juvenile patients developing induced or spontaneous gingivitis with healthy controls.Results: 36 supragingival biofilm samples from 9 adolescent gingivitis patients wearing orthodontic appliances (induced gingivitis), 40 supragingival plaques from 10 patients having spontaneous gingivitis, and 36 control samples from 9 individuals without gingivitis in the same age group were analyzed by 16S rRNA gene amplicon sequencing. Salivary microbiomes of the same persons were characterized by shotgun metagenome sequencing to compare the sessile, i.e. biofilm immobilized communities with planktonic microbiota. The amplicon and whole genome data sets were scrutinized using bioinformatics workflows designed to minimize systemic biases. RDP and RefSeq reference databases were compared in the identification of microbiome members.The composition and diversity of bacterial communities did not differ extensively between the two groups of gingivitis patients and controls. In spite of the overall similarities, the relative abundance of the genera Fusobacterium, Accermansia, Treponema and Campylobacter was prominently higher in samples from gingivitis patients versus controls. In contrast, the genera Lautropia, Kingella, Neisseria, Actinomyces and Rothia were significantly more abundant in controls than in either of the two gingivitis groups. Conclusions: The higher relative abundance of certain gingivitis-associated taxa may either reflect their role in disease pathogenesis or may indicate that gingival inflammation favored the selective overgrowth of distinct bacterial clusters. At any rate, the abundance pattern of certain taxa rather than individual strains shows characteristic features of potential diagnostic value. Stringent bioinformatics treatment of the sequencing data is mandatory to avoid unintentional misinterpretations.

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Gut microbiota markers associated with obesity and overweight in Italian adults

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Vanessa Palmas ◽  
Silvia Pisanu ◽  
Veronica Madau ◽  
Emanuela Casula ◽  
Andrea Deledda ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Smoking Status ◽  
16S Rrna Gene Sequencing ◽  
Normal Weight ◽  
Activity Level ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Obesity And Overweight ◽  
Rrna Gene Sequencing

AbstractIn the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.

scholarly journals Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

2021 ◽  
Vol 9 (4) ◽  
pp. 859
Author(s):  
Andrea Firrincieli ◽  
Andrea Negroni ◽  
Giulio Zanaroli ◽  
Martina Cappelletti
Keyword(s):  
Archaeal Community ◽  
Hydrocarbon Biodegradation ◽  
Natural Ecosystems ◽  
Central Mediterranean ◽  
Metabolic Potential ◽  
Metabolic Role ◽  
Sequencing Studies ◽  
Terrestrial Environments ◽  
Metagenome Sequencing ◽  
Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

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.

scholarly journals Early-Life Stress Modulates Gut Microbiota and Peripheral and Central Inflammation in a Sex-Dependent Manner

2021 ◽  
Vol 22 (4) ◽  
pp. 1899 ◽  
Author(s):  
Hae Jeong Park ◽  
Sang A. Kim ◽  
Won Sub Kang ◽  
Jong Woo Kim
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Life Stress ◽  
Early Life ◽  
Maternal Separation ◽  
Early Life Stress ◽  
Female Rats ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Male And Female Rats

Recent studies have reported that changes in gut microbiota composition could induce neuropsychiatric problems. In this study, we investigated alterations in gut microbiota induced by early-life stress (ELS) in rats subjected to maternal separation (MS; 6 h a day, postnatal days (PNDs) 1–21), along with changes in inflammatory cytokines and tryptophan-kynurenine (TRP-KYN) metabolism, and assessed the differences between sexes. High-throughput sequencing of the bacterial 16S rRNA gene showed that the relative abundance of the Bacteroides genus was increased and that of the Lachnospiraceae family was decreased in the feces of MS rats of both sexes (PND 56). By comparison, MS increased the relative abundance of the Streptococcus genus and decreased that of the Staphylococcus genus only in males, whereas the abundance of the Sporobacter genus was enhanced and that of the Mucispirillum genus was reduced by MS only in females. In addition, the levels of proinflammatory cytokines were increased in the colons (IFN-γ and IL-6) and sera (IL-1β) of the male MS rats, together with the elevation of the KYN/TRP ratio in the sera, but not in females. In the hippocampus, MS elevated the level of IL-1β and the KYN/TRP ratio in both male and female rats. These results indicate that MS induces peripheral and central inflammation and TRP-KYN metabolism in a sex-dependent manner, together with sex-specific changes in gut microbes.

scholarly journals Spontaneous Mutations That Confer Antibiotic Resistance inHelicobacter pylori

2001 ◽  
Vol 45 (3) ◽  
pp. 727-733 ◽  
Author(s):  
Ge Wang ◽  
Trevor J. M. Wilson ◽  
Qin Jiang ◽  
Diane E. Taylor
Keyword(s):  
Mutant Allele ◽  
Rapid Development ◽  
Mutagenic Effect ◽  
Serial Passage ◽  
Sublethal Dose ◽  
23S Rrna ◽  
Rrna Gene ◽  
Spontaneous Mutations ◽  
H Pylori

ABSTRACT In this study, we systematically examined in vitro frequencies and spectra of the spontaneous mutations in Helicobacter pylori that confer resistance to clarithromycin (Clar), metronidazole (Mtzr), amoxicillin (Amxr), ciprofloxacin (Cipr), and rifampin (Rifr). The mutation rate of Rifror Cipr determined in a fluctuation assay is 1 × 10−8 to 2 × 10−8 per cell per division. In contrast, the mutation rates of Clar, Mtzr, and Amxr are much lower (<10−9). However, Mtzr mutants could be readily selected in vitro by using the serial passage method, suggesting that the mutagenic effect and selective effect of a sublethal dose of metronidazole contribute to the rapid development of Mtzr. Analysis of spontaneous Rifr, Clar, and Cipr mutants confirmed previous results indicating that mutations within therpoB gene, the 23S rRNA gene, and thegyrA gene, respectively, are responsible; also, several new mutant alleles were identified. Mtzrmutants resulted most frequently, but not always, from mutations in the rdxA gene. DNA fragments containing each mutant allele could readily transform susceptibleH. pylori strains to resistance, confirming that each mutant allele is responsible for the resistance phenotype.

scholarly journals Faecal bacterial composition in horses with and without free faecal liquid: a case control study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katrin M. Lindroth ◽  
Johan Dicksved ◽  
Erik Pelve ◽  
Viveca Båverud ◽  
Cecilia E. Müller
Keyword(s):  
Relative Abundance ◽  
Case Control Study ◽  
Sampling Period ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Clostridioides Difficile ◽  
Liquid Phases ◽  
And Control ◽  
The 16S Rrna Gene ◽  
Control Study

AbstractFree faecal liquid (FFL) is a condition in horses which manifests as differential defecation of solid and liquid phases of faeces. The etiology of FFL is currently unknown, but deviances in the hindgut microbiota has been suggested to be of importance. The present study aimed to compare the faecal bacterial composition of farm-matched horses with (case, n = 50) and without (control, n = 50) FFL. Samples were collected at three different occasions. The V3 and V4 regions of the 16S rRNA gene were amplified and sequenced using Illumina sequencing. Also, samples were cultivated for detection of Clostridioides difficile and Clostridium perfringens. Analysis revealed similar faecal bacterial composition between case and control horses, but an effect of sampling period (p = 0.0001). Within sampling periods, 14 genera were present in higher or lower proportions in case compared to control horses in at least one sampling period. Compared to controls, case horses had higher relative abundance of Alloprevotella (adjusted p < 0.04) and lower relative abundance of Bacillus spp. (adjusted p < 0.03) in at least two sampling periods. All horses tested negative for C. difficile and C. perfringens by culture of faeces. Further studies are required to establish the clinical relevance of specific bacterial taxa in FFL.

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