scholarly journals Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns

2021 ◽  
Vol 10 (1) ◽  
pp. 11
Author(s):  
Anastasia A. Ivanova ◽  
Igor Y. Oshkin ◽  
Olga V. Danilova ◽  
Dmitriy A. Philippov ◽  
Nikolai V. Ravin ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Habitat Preferences ◽  
Rrna Gene ◽  
Comparative Genome Analysis ◽  
Raised Bogs ◽  
Negative Results ◽  
Rare Biosphere ◽  
Terrestrial Habitats ◽  
Northern Peatlands ◽  
Encoding Genes

Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.

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 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 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.

Use of aquatic plants by moose: sodium hunger or foraging efficiency?

1993 ◽  
Vol 71 (12) ◽  
pp. 2345-2351 ◽  
Author(s):  
James G. MacCracken ◽  
Victor Van Ballenberghe ◽  
James M. Peek
Keyword(s):  
Aquatic Plants ◽  
Habitat Preferences ◽  
Indirect Evidence ◽  
Foraging Efficiency ◽  
Aquatic Habitats ◽  
Forage Production ◽  
Sex Structure ◽  
Emergent Plants ◽  
Terrestrial Habitats ◽  
Emergent Species

Use of submergent aquatic plants by North American moose (Alces alces) has been linked to sodium hunger. Habitat preferences, seasonal diets, forage abundance and quality, and population surveys indicated that emergent plants in small shallow ponds were important to moose on the Copper River Delta, Alaska. However, sodium was abundant in terrestrial browse. We propose that foraging in aquatic habitats, particularly on emergent species, may be highly efficient based on the following habitat attributes and behavioral observations: (i) ponds dominated by either emergent or submergent species produced about 4 times more forage than terrestrial habitats, (ii) emergent and submergent plants were more digestible and had higher concentrations of minerals than browse, (iii) use of aquatic habitats followed trends in forage production over the growing season, (iv) indirect evidence suggested that forage intake rates were greater in aquatic habitats, and (v) use of aquatic habitats by male and female moose was in proportion to the sex structure of the population. These data provide consistent circumstantial evidence that use of emergent species, and possibly submergents, may maximize the intake of nutrients and also reduce conflicts between cropping forage and vigilance during a foraging bout.

A survey of terrestrial gastropods from central Maine

1976 ◽  
Vol 54 (5) ◽  
pp. 620-627 ◽  
Author(s):  
J. George Gleich ◽  
Frederick F. Gilbert
Keyword(s):  
Relative Abundance ◽  
Habitat Preferences ◽  
Coniferous Forests ◽  
Snail Species ◽  
Forest Types ◽  
Mixed Forests ◽  
Terrestrial Gastropods

Terrestrial gastropods were collected in central Maine from June to November 1971 to study their distribution, relative abundance, and habitat preferences. Gastropods were widespread, but not abundant. Thirty-five percent of the 1626 gastropods collected were slugs. Thirty-seven snail species, including eight slug species, were found. Discus cronkhitei and Zonitoides arboreus were the most commonly collected gastropods: Deroceras reliculatum and Pallifera dorsalis were the most common slugs. Snails (excluding slugs) were more abundant in the northwestern portion of central Maine, whereas slugs were more abundant in the southeastern portion. Slugs were significantly less abundant in coniferous forests than in deciduous or mixed forests, but snail numbers (excluding slugs) in the three forest types were not significantly different.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P &lt; 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

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