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Journal articles on the topic 'Firmicutes phylum'

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Author: Grafiati
Published: 9 March 2023

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1

Kozhieva, Madina, Natalia Naumova, Tatiana Alikina, Alexey Boyko, Valentin Vlassov, and Marsel R. Kabilov. "The Core of Gut Life: Firmicutes Profile in Patients with Relapsing-Remitting Multiple Sclerosis." Life 11, no. 1 (January 14, 2021): 55. http://dx.doi.org/10.3390/life11010055.

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The multiple sclerosis (MS) incidence rate has been increasing in Russia, but the information about the gut bacteriobiome in the MS-afflicted patients is scarce. Using the Illumina MiSeq sequencing of 16S rRNA gene amplicons, we aimed to analyze the Firmicutes phylum and its taxa in a cohort of Moscow patients with relapsing-remitting MS, assessing the effects of age, BMI, disease modifying therapy (DMT), disability (EDSS), and gender. Among 1252 identified bacterial OTUs, 857 represented Firmicutes. The phylum was the most abundant also in sequence reads, overall averaging 74 ± 13%. The general linear model (GLM) analysis implicated Firmicutes/Clostridia/Clostridiales/Lachospiraceae/Blautia/Blautia wexlerae as increasing with BMI, and only Lachospiraceae/Blautia/Blautia wexlerae as increasing with age. A marked DMT-related decrease in Firmicutes was observed in females at the phylum, class (Clostridia), and order (Clostridiales) levels. The results of our study implicate DMT and gender as factors shaping the fecal Firmicutes assemblages. Together with the gender-dependent differential MS incidence growth rate in the country, the results suggest the likely involvement of gender-specific pathoecological mechanisms underlying the occurrence of the disease, switching between its phenotypes and response to disease-modifying therapies. Overall, the presented profile of Firmicutes can be used as a reference for more detailed research aimed at elucidating the contribution of this core phylum and its lower taxa into the etiology and progression of relapsing-remitting multiple sclerosis.
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2

Tsai, Hui-Ju, Yi-Chun Tsai, Wei-Wen Hung, Wei-Chun Hung, Chen-Chia Chang, and Chia-Yen Dai. "Gut Microbiota and Non-Alcoholic Fatty Liver Disease Severity in Type 2 Diabetes Patients." Journal of Personalized Medicine 11, no. 3 (March 23, 2021): 238. http://dx.doi.org/10.3390/jpm11030238.

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Introduction: Non-alcoholic fatty liver disease (NAFLD) remains an important health issue worldwide. The increasing prevalence of NAFLD is linked to type 2 diabetes (T2D). The gut microbiota is associated with the development of NAFLD and T2D. However, the relationship between gut microbiota and NAFLD severity has remained unclear in T2D patients. The aim of this study was to evaluate the relationship of gut microbiota with the severity of NAFLD in T2D patients. Methods: This cross-sectional study used transient elastography (FibroScan) to evaluate the severity of hepatic steatosis. We utilized qPCR to measure the abundance of Bacteroidetes, Firmicutes, Faecalibacterium prausnitzii, Clostridium leptum group, Bacteroides, Bifidobacterium, Akkermansia muciniphila, and Escherichia coli. Results: Of 163 T2D patients, 83 with moderate to severe NAFLD had higher abundance of bacteria of the phylum Firmicutes with respect to 80 patients without NAFLD or with mild NAFLD. High abundance of the phylum Firmicutes increased the severity of NAFLD in T2D patients. A positive correlation between NAFLD severity and the phylum Firmicutes was found in T2D male patients with body mass index ≥24 kg/m2 and glycated hemoglobin <7.5%. Conclusion: Enrichment of the fecal microbiota with the phylum Firmicutes is significantly and positively associated with NAFLD severity in T2D patients. The gut microbiota is a potential predictor of NAFLD severity in T2D patients.
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3

Wirth, Roland, Nikolett Bódi, Zita Szalai, Lalitha Chandrakumar, Gergely Maróti, Kornél L. Kovács, Zoltán Bagi, Diána Mezei, János Balázs, and Mária Bagyánszki. "Perturbation of the mucosa-associated anaerobic gut microbiota in streptozotocin-induced diabetic rats." Acta Biologica Szegediensis 65, no. 1 (August 21, 2021): 75–84. http://dx.doi.org/10.14232/abs.2021.1.75-84.

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Our aim was to map the gut region-specific differences of the mucosa-associated microbiome distribution in a streptozotocin-induced diabetic rat model. Tissue samples from the duodenum, ileum and colon were collected 10 weeks after the onset of hyperglycaemia to analyse the mucosa-associated microbiota using next-generation DNA sequencing. Striking differences were observed in the mucosa-associated microbiota of the duodenum between diabetic and control rats. A significant invasion of the aerobic genus Mycoplasma was apparent in diabetes, and the abundance of the anaerobic phylum Firmicutes decreased massively. It is noteworthy that insulin treatment eliminated the Mycoplasma invasion in the duodenum and apparently restored the anaerobic environment in the mucosa. In the ileum the abundance of the phylum Firmicutes increased in the diabetic samples. Although the proportion of the phylum Proteobacteria decreased moderately, its composition changed significantly, and insulin treatment induced only minor alterations. In the diabetic samples of colon, the abundance of the phylum Firmicutes decreased slightly, the relative number of the bacteria in the phylum Bacteroidetes increased strongly as compared to the control values, and after insulin treatment this increase was more significant. Chronic hyperglycaemia has the most prominent effect on the mucosa-associated microbiota in the duodenum.
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Seong, Chi Nam, Joo Won Kang, Ji Hee Lee, So Yeon Seo, Jung Jae Woo, Chul Park, Kyung Sook Bae, and Mi Sun Kim. "Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea." Journal of Microbiology 56, no. 1 (January 2018): 1–10. http://dx.doi.org/10.1007/s12275-018-7318-x.

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5

Lauková, Andrea, Lenka Micenková, Monika Pogány Simonová, Valentína Focková, Jana Ščerbová, Martin Tomáška, Emília Dvorožňáková, and Miroslav Kološta. "Microbiome Associated with Slovak Traditional Ewe’s Milk Lump Cheese." Processes 9, no. 9 (September 7, 2021): 1603. http://dx.doi.org/10.3390/pr9091603.

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Worldwide consumers increasingly demand traditional/local products, to which those made from ewe’s milk belong. In Slovakia, dairy products made from ewe’s milk have a long tradition. A total of seventeen farmhouse fresh ewe’s milk lump cheeses from various local farm producers in central Slovakia were sampled at farms and then analyzed. Based on the sequencing data analysis, the phylum Firmicutes dominated (60.92%) in ewe’s lump cheeses, followed with the phylum Proteobacteria (38.23%), Actinobacteria (0.38%) and Bacteroidetes (0.35%). The phylum Firmicutes was represented by six genera, among which the highest amount possessed the genus Streptococcus (41.13%) followed with the genus Lactococcus (8.54%), Fructobacillus (3.91%), Enterococcus (3.18%), Staphylococcus (1.80%) and the genus Brochotrix (0.08%). The phylum Proteobacteria in ewe’s lump cheeses involved eight Gram-negative genera: Pseudomonas, Acinetobacter, Enterobacter, Ewingella, Escherichia-Shigella, Pantoea and Moraxella. The phylum Bacteroidetes involved three genera: Bacteroides, Sphingobacterium and Chrysobacterium. Results presented are original; the microbiome of Slovak ewe’s milk lump cheese has been not analyzed at those taxonomic levels up to now.
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6

Zhao, Siyue, Caiwu Li, Guo Li, Shengzhi Yang, Yingming Zhou, Yongguo He, Daifu Wu, et al. "Comparative analysis of gut microbiota among the male, female and pregnant giant pandas (Ailuropoda Melanoleuca)." Open Life Sciences 14, no. 1 (July 23, 2019): 288–98. http://dx.doi.org/10.1515/biol-2019-0032.

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AbstractThe giant panda (GP) was the most endangered species in China, and gut microbiota plays a vital role in host health. To determine the differences of the gut microbiota among the male, female and pregnant GPs, a comparative analysis of gut microbiota in GPs was carried out by 16S rRNA and ITS high-throughput sequencing. In 16S rRNA sequencing, 435 OTUs, 17 phyla and 182 genera were totally detected. Firmicutes (53.6%) was the predominant phylum followed by Proteobacteria (37.8%) and Fusobacteria (7.1%). Escherichia/Shigella (35.9%) was the most prevalent genus followed by Streptococcus (25.9%) and Clostridium (11.1%). In ITS sequencing, 920 OTUs, 6 phyla and 322 genera were also detected. Ascomycota (71.3%) was the predominant phylum followed by Basidiomycota (28.4%) and Zygomycota (0.15%). Purpureocillium (4.4%) was the most prevalent genus followed by Cladosporium (2.5%) and Pezicula (2.4%). Comparative analysis indicated that the male GPs harbor a higher abundance of phylum Firmicutes than female GPs with the contribution from genus Streptococcus. Meanwhile, the female GPs harbor a higher abundance of phylum Proteobacteria than male GPs with the contribution from genus Escherichia/ Shigella. In addition, the shift in bacteria from female to pregnant GPs indicated that phylum Firmicutes increased significantly with the contribution from Clostridium in the gut, which may provide an opportunity to study possible associations with low reproduction of the GPs.
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Xu, Huiwen, Lucas Jurado-Fasoli, Lourdes Ortiz-Alvarez, Francisco J. Osuna-Prieto, Isabelle Kohler, Xinyu Di, Ramiro Vilchez-Vargas, et al. "Plasma Levels of Omega-3 and Omega-6 Derived Oxylipins Are Associated with Fecal Microbiota Composition in Young Adults." Nutrients 14, no. 23 (November 24, 2022): 4991. http://dx.doi.org/10.3390/nu14234991.

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Pre-clinical studies suggest that circulating oxylipins, i.e., the oxidation products of polyunsaturated fatty acids (PUFAs), modulate gut microbiota composition in mice, but there is no information available in humans. Therefore, this study aimed to investigate the relationship between omega-3 and omega-6 derived oxylipins plasma levels and fecal microbiota composition in a cohort of young adults. 80 young adults (74% women; 21.9 ± 2.2 years old) were included in this cross-sectional study. Plasma levels of oxylipins were measured using liquid chromatography-tandem mass spectrometry. Fecal microbiota composition was analyzed by V3-V4 16S rRNA gene sequencing. We observed that plasma levels of omega-3 derived oxylipins were positively associated with the relative abundance of Clostridium cluster IV genus (Firmicutes phylum; rho ≥ 0.415, p ≤ 0.009) and negatively associated with the relative abundance of Sutterella genus (Proteobacteria phylum; rho ≥ −0.270, p ≤ 0.041), respectively. Moreover, plasma levels of omega-6 derived oxylipins were negatively associated with the relative abundance of Acidaminococcus and Phascolarctobacterium genera (Firmicutes phylum; all rho ≥ −0.263, p ≤ 0.024), as well as Sutterella, Succinivibrio, and Gemmiger genera (Proteobacteria phylum; all rho ≥ −0.263, p ≤ 0.024). Lastly, the ratio between omega-6 and omega-3 oxylipins plasma levels was negatively associated with the relative abundance of Clostridium cluster IV genus (Firmicutes phylum; rho = −0.334, p = 0.004) and Butyricimonas genus (Bacteroidetes phylum; rho = −0.292, p = 0.014). In conclusion, our results show that the plasma levels of omega-3 and omega-6 derived oxylipins are associated with the relative abundance of specific fecal bacteria genera.
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Tsai, Hui-Ju, Wei-Chung Tsai, Wei-Chun Hung, Wei-Wen Hung, Chen-Chia Chang, Chia-Yen Dai, and Yi-Chun Tsai. "Gut Microbiota and Subclinical Cardiovascular Disease in Patients with Type 2 Diabetes Mellitus." Nutrients 13, no. 8 (August 1, 2021): 2679. http://dx.doi.org/10.3390/nu13082679.

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Type 2 diabetes (T2D) is associated with an increased risk of cardiovascular disease (CVD). The gut microbiota may contribute to the onset and progression of T2D and CVD. The aim of this study was to evaluate the relationship between the gut microbiota and subclinical CVD in T2D patients. This cross-sectional study used echocardiographic data to evaluate the cardiac structure and function in T2D patients. We used a quantitative polymerase chain reaction to measure the abundances of targeted fecal bacterial species that have been associated with T2D, including Bacteroidetes, Firmicutes, Clostridium leptum group, Faecalibacterium prausnitzii, Bacteroides, Bifidobacterium, Akkermansia muciniphila, and Escherichia coli. A total of 155 subjects were enrolled (mean age 62.9 ± 10.1 years; 57.4% male and 42.6% female). Phyla Bacteroidetes and Firmicutes and genera Bacteroides were positively correlated with the left ventricular ejection fraction. Low levels of phylum Firmicutes were associated with an increased risk of left ventricular hypertrophy. High levels of both phylum Bacteroidetes and genera Bacteroides were negatively associated with diastolic dysfunction. A high phylum Firmicutes/Bacteroidetes (F/B) ratio and low level of genera Bacteroides were correlated with an increased left atrial diameter. Phyla Firmicutes and Bacteroidetes, the F/B ratio, and the genera Bacteroides were associated with variations in the cardiac structure and systolic and diastolic dysfunction in T2D patients. These findings suggest that changes in the gut microbiome may be the potential marker of the development of subclinical CVD in T2D patients.
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9

Neupane, Saraswoti, Anuradha Ghosh, Sebastian Gunther, Karin Martin, and Ludek Zurek. "Culicoidibacter larvae gen. nov., sp. nov., from the gastrointestinal tract of the biting midge (Culicoides sonorensis) larva, belongs to a novel lineage Culicoidibacteraceae fam. nov., Culicoidibacterales ord. nov. and Culicoidibacteria classis nov. of the phylum Firmicutes." International Journal of Systematic and Evolutionary Microbiology 70, no. 12 (December 1, 2020): 6482–90. http://dx.doi.org/10.1099/ijsem.0.004543.

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Strain CS-1T, a novel facultative anaerobic bacterium, was isolated from the larval gastrointestinal tract of the biting midge, Culicoides sonorensis, a vector of the epizootic haemorrhagic disease virus and the bluetongue virus. Cells were Gram-stain-positive, non-motile, non-spore-forming, pleomorphic rods. Optimal growth occurred at pH 7.5 and 37 °C. The G+C content of the genomic DNA was 38.3 mol%, estimated by using HPLC. The dominant cellular fatty acids were C14 : 0 (45.9 %) and C16 : 0 (26.6 %). The polar lipid profile comprised glycolipids, diphosphatidylglycerol, phospholipids and phosphoglycolipids. Respiratory quinones were not detected. Strain CS-1T had very low 16S rRNA gene similarity to members of the phylum Firmicutes : Macrococcus canis KM45013T (85 % similarity) and Turicibacter sanguinis MOL361T (88 % similarity). Phylogenetic analysis based on 16S rRNA, rpoB, gyrB genes, and conserved protein sequences of the whole genome revealed that strain CS-1T was related to members of the classes Bacilli and Erysipelotrichia within the phylum Firmicutes . Furthermore, average nucleotide identity and digital DNA–DNA hybridization analyses of the whole genome revealed very low sequence similarity to species of Bacilli and Erysipelotrichaceae ( Macrococcus canis KM45013T and Turicibacter sp. H121). These results indicate that strain CS-1T belongs to the phylum Firmicutes and represents a new species of a novel genus, family, order and class. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, we propose the novel taxon Culicoidibacter larvae gen. nov., sp. nov. with the type strain CS-1T (=CCUG 71726T=DSM 106607T) within the hereby new proposed novel family Culicoidibacteraceae fam. nov., new order Culicoidibacaterales ord. nov. and new class Culicoidibacteria classis nov. in the phylum Firmicutes .
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10

Haakensen, M., C. M. Dobson, H. Deneer, and B. Ziola. "Real-time PCR detection of bacteria belonging to the Firmicutes Phylum." International Journal of Food Microbiology 125, no. 3 (July 2008): 236–41. http://dx.doi.org/10.1016/j.ijfoodmicro.2008.04.002.

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11

Kunisawa, Takashi. "Evolutionary relationships of completely sequenced Clostridia species and close relatives." International Journal of Systematic and Evolutionary Microbiology 65, Pt_11 (November 1, 2015): 4276–83. http://dx.doi.org/10.1099/ijsem.0.000638.

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The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.
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12

Panosyan, H. H. "BACTERIAL PROFILES OF KARVACHAR HOT SPRING IDENTIFIED BY COMBINATION OF DIFFERENT MOLECULAR APPROACHES." Proceedings of the YSU B: Chemical and Biological Sciences 54, no. 2 (252) (August 17, 2020): 147–53. http://dx.doi.org/10.46991/pysu:b/2020.54.2.147.

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Molecular techniques, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA genes clone library construction and metagenomic analysis, were used to describe the bacterial composition of the Karvachar geothermal spring. It was shown the predominance of bacteria belonging to the phyla Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria in the studied spring. Representatives of phylum Firmicutes were not detected in the clone library, while DGGE profiling and metagenome analysis confirmed the presence of Firmicutes as one of the major components in the bacterial community.
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Carlier, Jean-Philippe, Guylène K'ouas, Isabelle Bonne, Alain Lozniewski, and Francine Mory. "Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)." International Journal of Systematic and Evolutionary Microbiology 54, no. 5 (September 1, 2004): 1611–15. http://dx.doi.org/10.1099/ijs.0.63060-0.

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A hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family ‘Lachnospiraceae’ within the phylum Firmicutes. Oribacterium gen. nov. is proposed for this group of organisms and Oribacterium sinus gen. nov. sp. nov. for strain AIP 354.02T (=CIP 107991T=CCUG 48084T).
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Geng, Jianing, Sainan Luo, Hui-Ru Shieh, Hsing-Yi Wang, Songnian Hu, and Yi-Ywan M. Chen. "Identification of a Putative CodY Regulon in the Gram-Negative Phylum Synergistetes." International Journal of Molecular Sciences 23, no. 14 (July 18, 2022): 7911. http://dx.doi.org/10.3390/ijms23147911.

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CodY is a dominant regulator in low G + C, Gram-positive Firmicutes that governs the regulation of various metabolic pathways and cellular processes. By using various bioinformatics analyses and DNA affinity precipitation assay (DAPA), this study confirmed the presence of CodY orthologues and corresponding regulons in Gram-negative Synergistetes. A novel palindromic sequence consisting of AT-rich arms separated by a spacer region of variable length and sequence was identified in the promoters of the putative codY-containing operons in Synergistetes. The consensus sequence from genera Synergistes and Cloacibacillus (5′-AATTTTCTTAAAATTTCSCTTGATATTTACAATTTT) contained three AT-rich regions, resulting in two palindromic sequences; one of which is identical to Firmicutes CodY box (5′-AATTTTCWGAAAATT). The function of the consensus sequence was tested by using a recombinant CodY protein (His-CodYDSM) of Cloacibacillus evryensis DSM19522 in DAPA. Mutations in the central AT-rich sequence reduced significantly the binding of His-CodYDSM, whereas mutations in the 5′ or 3′ end AT-rich sequence slightly reduced the binding, indicating that CodYDSM could recognize both palindromic sequences. The proposed binding sequences were found in the promoters of multiple genes involved in amino acids biosynthesis, metabolism, regulation, and stress responses in Synergistetes. Thus, a CodY-like protein from Synergistetes may function similarly to Firmicutes CodY.
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Zulhaerati, Zulhaerati, Sri Budiarti, and Rika Indri Astuti. "Metagenomic Analysis of Bacteria Phylum Firmicutes and Bacteroidetes in Women with Type 2 Diabetes." HAYATI Journal of Biosciences 26, no. 3 (December 2, 2019): 110. http://dx.doi.org/10.4308/hjb.26.3.110.

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Diabetes mellitus (DM) is a serious health problem in Indonesia. Type 2 diabetes is a metabolic disease which primarily caused by obesity-linked insulin resistance. There is a link between insulin resistance and bacterial populations in the gut. Therefore, the aims of this study was to analyze composition of bacteria belong to the phylum Firmicutes and Bacteroidetes in women with type 2 diabetes and non-diabetic persons as control. The study included five female adults type 2 diabetes patients and five healthy controls. The bacteria composition was analyzed for abundance by denaturing gradient gel electrophoresis (DGGE). Metagenomic analysis based on 16S rRNA gene was represented by 12 DGGE bands. The twelve respective bands showed the similarity ranging from 77 up to 98%. Diversity of microbial composition in women type 2 diabetes was represented by five DGGE bands are Bacteroides fragilis, Bacteroides vulgatus, uncultured Bacteroides sp. clone Lb4eF4, uncultured bacterium clone 16sms90-5g05, and uncultured bacterium clone Malaga 1F14. Four DGGE bands in women healthy controls are closely related to uncultured bacterium isolate DGGE gel band Eub42, uncultured bacterium isolate DGGE gel band K115, uncultured bacterium clone HFV04255, and Enterococcus sp. the finding shows bacterial species belong to the phylum Bacteroidetes was mostly found in women diabetic group, while those belong to the phylum Firmicutes was mostly found in healthy controls.
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Jumas-Bilak, E., L. Roudiere, and H. Marchandin. "Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'." INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 59, no. 5 (April 30, 2009): 1028–35. http://dx.doi.org/10.1099/ijs.0.006718-0.

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Jumas-Bilak, Estelle, Hélène Marchandin, and Laurent Roudière. "Description of ‘Synergistetes’ phyl. nov. and emended description of the phylum ‘Deferribacteres’ and of the family Syntrophomonadaceae, phylum ‘Firmicutes’." International Journal of Systematic and Evolutionary Microbiology 59, no. 7 (July 1, 2009): 1851. http://dx.doi.org/10.1099/00207713-59-7-1851-a.

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Jean-Pierre LEPARGNEUR. "LACTOBACILLUS." ACTUALITES PERMANENTES EN MICROBIOLOGIE CLINIQUE 18, no. 04 (December 1, 2019): 6. http://dx.doi.org/10.54695/apmc.18.04.1523.

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Ils appartiennent au domaine des bactéries, phylum B13 :les Firmicutes (Gram positif avec DNA G + C faible); ils sontde la classe 3, ordre des lactobacillales (qui comprend 5famillesphylogénétiquement cohérentes), famille des Lactobacillaceae,genre Lactobacillus (selon Garrity, 2005)
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Yadav, Brijesh, Poonam Yadav, Muneendra Kumar, Shalini Vasvani, Mukul Anand, Avinash Kumar, Dilip Kumar Swain, Sarvajeet Yadav, and Arun Kumar Madan. "Effect of Heat Stress on Rumen Microbial Diversity and Fermentation Pattern in Buffalo." Advanced Gut & Microbiome Research 2022 (November 11, 2022): 1–14. http://dx.doi.org/10.1155/2022/1248398.

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In this study, changes in rumen microbiome and fermentation were examined during heat stress (HS) in buffaloes. Six buffalo heifers were exposed to thermoneutral ( THI = 72 ) and HS ( THI = 87 – 90 ) conditions for 6 h between 10 AM and 4 PM for 21 days in the climatic chamber. A digestibility trial with four-day collection period was conducted at the end of the study, and rumen liquor was collected on day 21. At the phylum level, an increased ( p < 0.05 ) abundance of Firmicutes and a decreased ( p < 0.05 ) abundance of Proteobacteria and Planctomycetes were observed during HS compared to thermoneutral conditions. The abundance of 6 different genera of phylum Firmicutes, YRC22 (phylum Bacteroidetes), and Stenotrophomonas (phylum Proteobacteria) was increased ( p < 0.05 ), whereas B. firmus, Lysinibacillus, Bacteroides unclassified genus (family Enterobacteriaceae), and Methanobrevibacter decreased ( p < 0.05 ) during HS compared to control. Eight new genera from four different phyla were detected after HS exposure, whereas one genus was not detected in the rumen after HS exposure, which was present during thermoneutral conditions. Dry matter intake, volatile fatty acid concentration, and digestibility did not change ( p > 0.05 ) during HS. It can be concluded that the resilience of the rumen microbial population invokes adaptive responses by changing their abundance to minimize the adverse effects on fermentation and digestibility in buffalo heifers.
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Govil, Tanvi, Manasi Paste, Dipayan Samanta, Aditi David, Kian Mau Goh, Xiangkai Li, David R. Salem, and Rajesh K. Sani. "Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA." Microorganisms 9, no. 1 (January 6, 2021): 113. http://dx.doi.org/10.3390/microorganisms9010113.

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Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of the Firmicutes in two distinctly related environmental samples—South Dakota Landfill Compost (SDLC, 60 °C), and Sanford Underground Research Facility sediments (SURF, 45 °C). Although distinct microbial community compositions were observed, there was a dominance of Firmicutes in both the SDLC and SURF samples, followed by Proteobacteria. The abundant classes of bacteria in the SDLC site, within the phylum Firmicutes, were Bacilli (83.2%), and Clostridia (2.9%). In comparison, the sample from the SURF mine was dominated by the Clostridia (45.8%) and then Bacilli (20.1%). Within the class Bacilli, the SDLC sample had more diversity (a total of 11 genera with more than 1% operational taxonomic unit, OTU). On the other hand, SURF samples had just three genera, about 1% of the total population: Bacilli, Paenibacillus, and Solibacillus. With specific regard to Geobacillus, it was found to be present at a level of 0.07% and 2.5% in SURF and SDLC, respectively. Subsequently, culture isolations of endospore-forming Firmicutes members from these samples led to the isolation of a total of 117 isolates. According to colony morphologies, and identification based upon 16S rRNA and gyrB gene sequence analysis, we obtained 58 taxonomically distinct strains. Depending on the similarity indexes, a gyrB sequence comparison appeared more useful than 16S rRNA sequence analysis for inferring intra- and some intergeneric relationships between the isolates.
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Han, Ji-Hye, Yochan Joung, Tae-Su Kim, Jin-Woo Bae, Chang-Jun Cha, Jongsik Chun, Wan-Taek Im, et al. "Report on 24 unrecorded bacterial species of Korea belonging to the phylum Firmicutes." Journal of Species Research 4, no. 2 (August 30, 2015): 127–36. http://dx.doi.org/10.12651/jsr.2015.4.2.127.

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Cholewińska, Paulina, Marta Michalak, Konrad Wojnarowski, Szymon Skowera, Jakub Smoliński, and Katarzyna Czyż. "Levels of Firmicutes, Actinobacteria Phyla and Lactobacillaceae Family on the Skin Surface of Broiler Chickens (Ross 308) Depending on the Nutritional Supplement and the Housing Conditions." Agriculture 11, no. 4 (March 26, 2021): 287. http://dx.doi.org/10.3390/agriculture11040287.

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The microbiome of animals, both in the digestive tract and in the skin, plays an important role in protecting the host. The skin is one of the largest surface organs for animals; therefore, the destabilization of the microbiota on its surface can increase the risk of diseases that may adversely affect animals’ health and production rates, including poultry. The aim of this study was to evaluate the effect of nutritional supplementation in the form of fermented rapeseed meal and housing conditions on the level of selected bacteria phyla (Firmicutes, Actinobacteria, and family Lactobacillaceae). The study was performed on 30 specimens of broiler chickens (Ross 308), individually kept in metabolic cages for 36 days. They were divided into 5 groups depending on the feed received. On day 36, skin swabs were individually collected. Temperature and humidity were measured in the room. The temperature was measured every 2 days (18 measurements × 6 points). The results of Real-Time PCR analysis have shown a significant effect of the feed additive on the level of Firmicutes phylum on the skin. On the other hand, a variable level of the tested bacteria was shown depending on the location of the cages. The Firmicutes phylum and Lactobacillaceae family achieved the highest level in the top-window zone. However, in the case of the Actinobacteria phylum, the highest level was found at the top-door and middle-door zones. The obtained results suggest that the conditions in which animals live may affect the microbiota of their skin.
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Bobkova, Veronika, Sergey Konovalov, and Mikhail Upadyshev. "Phylogenetic diversity of the endophytic bacterial component of the microbiome of apple clonal rootstocks during in vitro reproduction and cultivation under various agroecological conditions." BIO Web of Conferences 34 (2021): 04009. http://dx.doi.org/10.1051/bioconf/20213404009.

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The phylogenetic diversity of the endophytic bacterial component of the clonal apple rootstock microbiome 57-490 and 54-118 was studied for microplants and 5-year-old plants grown from the same tissue culture and growing on sod-podzolic soils of different granulometric composition with different chemical, physicochemical and physical properties. Proteobacteria (91.6%) in rootstock 57-490, Proteobacteria (52.5%) and Firmicutes (47.4%) in rootstock 54-118 are the predominant phylum of endophytic bacteria in apple rootstock plant tissues in vitro culture. The relative amount of phylum Firmicutes endophytic bacteria, in comparison with in vitro culture, decreases in the roots to 0.7-2.0%, and even more significantly in the leaves (to 0-0.2%). At cultivation on heavy loamy soil, endophytic bacteria belonging to the phylum Actinobacteriota (11.7%) are found in the studied rootstock roots, the relative content of which, when grown on medium loamy soil, in the roots decreases to 2.7-4.1%, in the leaves – to 0,1-0.2%. The data show that in the endosphere of the culture in vitro, the diversity and uniformity of the community of endophytic bacteria is significantly lower (Shannon index 0.42-1.00) than in the roots of rootstocks grown in the outdoor growing (1.34-2.08). For leaves, the Shannon index is characterized by the lowest values (0.06-0.13).
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Marchandin, Hélène, Corinne Teyssier, Josiane Campos, Hélène Jean-Pierre, Frédéric Roger, Bernard Gay, Jean-Philippe Carlier, and Estelle Jumas-Bilak. "Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes." International Journal of Systematic and Evolutionary Microbiology 60, no. 6 (June 1, 2010): 1271–79. http://dx.doi.org/10.1099/ijs.0.013102-0.

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Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388T (=AIP 149.07T=CIP 109806T=DSM 21255T=CCUG 56017T) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes ‘Bacilli’, ‘Clostridia’, Thermolithobacteria and ‘Erysipelotrichi’ in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.
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Shoshina, Oksana, Elena Shejjda, Elvina Shajahmetova, Svyatoslav Lebedev, Galimzhan Duskaev, and Olga Kvan. "PSVI-13 Changes in the taxonomic composition of the rumen of ruminants when introducing fat components into the diet." Journal of Animal Science 99, Supplement_3 (October 8, 2021): 232. http://dx.doi.org/10.1093/jas/skab235.424.

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Abstract Fats are concentrated energy sources for cattle growth, but their inclusion in the diet has a huge impact on the taxonomic composition of the rumen. The aim of this study was to evaluate the effect of supplemental linseed oil administration (3% of dry matter (DM) diet) on microbiota and DM digestibility in the rumen. The studies carried out on Kazakh white-headed bull calves, aged 15 months, with chronic rumen fistula (diet - 70% grassland hay, 30% barley grain). Dietary dry matter digestibility (in-vitro in an artificial rumen system, for 24 hours) analyzed daily for 10 days, and microflora (fluid-bound) analyzed using high-throughput 16SrRNA gene sequencing (Illumina). Inclusion of LO showed a slight 3.5% increase in DM digestibility compared to C (52.0% versus 53.9%). The taxonomic composition of the rumen microbiocenosis in group C was mainly represented by the phylum Firmicutes (54.7%) and Bacteroidetes (39.3%), while other phylum numbers were less than 2%. When LO was injected, the dominance of phylum Bacteroidetes (64.2%), phylum Firmicutes (19.3%), and Verrucomicrobia (5.3%) was noted. The calculation of the Shannon index showed an increase in species diversity in the group that received LO. It was H’= 0.76, while in CH’= 0.42. The Simpson dominance index in group C was 0.44, in the group receiving LOD = 0.54. The obtained data show a positive effect. The linseed oil allow to increase the biodiversity of the rumen microbiome and the digestibility of DM feed, which can be used in fattening young cattle. This research performed with financial support from the project 0761-2019-0005.
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Imperatore, Roberta, Baldassare Fronte, Daniel Scicchitano, Graziella Orso, Maria Marchese, Serena Mero, Rosario Licitra, Elena Coccia, Marco Candela, and Marina Paolucci. "Dietary Supplementation with a Blend of Hydrolyzable and Condensed Tannins Ameliorates Diet-Induced Intestinal Inflammation in Zebrafish (Danio rerio)." Animals 13, no. 1 (December 31, 2022): 167. http://dx.doi.org/10.3390/ani13010167.

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The current study evaluated the effects of hydrolyzable and condensed tannins from chestnut and quebracho wood, respectively (TSP, Silvafeed®), on zebrafish with intestinal inflammation induced by a plant-based diet (basal diet). Four experimental diets were prepared as follows: the basal diet + 0 TSP, the basal diet + TSP at 0.9 g/kg of feed, the basal diet + TSP at 1.7 g/kg of feed, and the basal diet + TSP at 3.4 g/kg of feed. Eighty-four zebrafish (Danio rerio) were fed for 12 days with the experimental diets. In zebrafish fed the basal diet, intestine integrity appeared to be altered, with damaged intestinal villi, high immunoexpression of tumor necrosis factor-α (TNFα) and cyclooxygenase 2 (COX2), and high expression of the cox2, interleukin 1 (il-1b), interleukin 8 (cxcl8-l1), and tnfα genes. The tannin treatment partially restored intestinal morphology and downregulated the expression of cytokines. The best activity was detected with 1.7 and 3.4 g/kg of feed. In the guts of all groups, Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes were the most represented phyla. The most represented genera were Plesiomonas and Sphingomonas, belonging to the Proteobacteria phylum; Cetobacterium, belonging to the Fusobacteria phylum; and Lactobacillus, belonging to the Firmicutes phylum. No significant differences were detected among groups, except for a slight decrease in the Fusobacteria phylum and slight increases in the Shewanella and Bacteroides genera with TSP. In conclusion, these results suggest that tannins can improve the zebrafish intestinal inflammation caused by a terrestrial-plant-based diet in a dose-dependent manner.
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Kim, Eunji, Sungmi Choi, Jin-Woo Bae, Chang-Jun Cha, Wan-Taek Im, Kwang-Yeop Jahng, Ki-seong Joh, and Hana Yi. "A report of 10 unrecorded bacterial species of Korea, belonging to the phylum Firmicutes." Journal of Species Research 5, no. 2 (June 30, 2016): 235–40. http://dx.doi.org/10.12651/jsr.2016.5.2.235.

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Sharma, Mukesh Kumar. "Metagenomic analysis of oral microbiota among oral cancer patients and tobacco chewers in Rajasthan, India." Bioinformation 18, no. 9 (September 30, 2022): 757–63. http://dx.doi.org/10.6026/97320630018757.

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Data on the microbial composition among tobacco chewers and oral cancer patients in Rajasthan, India is of interest. NGS analysis from tobacco chewers and oral cancer comprised the most abundant and core microbial taxa in the oral cavity. It shows that highly pathogenic phylum consisting of 6% Fusobacteria and 9% Firmicutes are observed in oral cancer samples; whereas, 0.6% Treponema, 34% Firmicutes, 0.02% Mollicutes, and 4% Fusobacteria are seen in tobacco chewers. Thus, data shows that the most abundant and core microbial taxa are found in the oral cavity of tobacco chewers and oral cancer patients in Rajasthan, India.
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Seol, Mijin, Yu Ra Lee, Kyung Mi Kim, Cheol Min Shin, Hyuk Yoon, Jae Ho Cho, Dong Jin Song, Nayoung Kim, Young Soo Park, and Dong Ho Lee. "The difference of the gut microbiota of gastric cancer in relation to Helicobacter pylori negativity and positivity." Journal of Clinical Oncology 37, no. 4_suppl (February 1, 2019): 10. http://dx.doi.org/10.1200/jco.2019.37.4_suppl.10.

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10 Background: Helicobacter pylori (HP) is a major risk factor for gastric cancer, however, only 1-2% of HP(+) people develop adenocarcinoma. In this study, we have compared the intestinal microbiota composition related to HP status among gastric cancer patient using 16SrRNA gene-based metagenomic sequencing analysis and culture-based method. Methods: Stool samples were collected from 18 gastric cancer patients. 16S rRNA genes were sequenced on the Illumina Miseq platform and further analyzed to evaluate the gut bacterial community. The bacteria strains of fecal sample were isolated in aerobic and anaerobic condition. Results: Metagenomics analysis of fecal sample showed four major phyla; Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were dominant. Firmicutes were the most dominant phylum. Within this phylum, the relative abundance of Clostridiales including Ruminococcus was higher in the HP(-) group, whereas Lactobacillales including streptococcus was higher in HP(+) group. In addition the relative abundance of Bacteroidetes in HP(-) group and Actinobacteria (especially, genus Bifidobacterium) in HP(+) group was observed highly. In the bacterial culture-based approach, bacteria strains belonged to Clostridiales such as Clostridium perfringens, Ruminococcus feacis, Blautia sp., Coprococcus comes were isolated in HP(-) sample. In HP(+) sample, Klebsiella, Bacteroides, Bifidobacterium were isolated. Bacillus species, Escherichia/Shigella was enriched regardless of HP exist. Streptococcus was not cultivated in HP(+) group, but isolated in HP(-) group in contrast with metagenome data. Conclusions: We found the intestinal bacterial diversity in the HP(+) group was lower than those in the HP(-) and the microbial composition was different between HP(+) and HP(-). Metagenome analysis showed the order Clostridiales of the phylum Firmicutes were enriched in the HP(-) group while the order Lactobacillales (specially, Streptococcus) were enriched in the HP(+) group. Compared to isolates between two groups, bacteria species belonged to the order Clostridiales such as Clostridium, Ruminococcus , Blautia , Coprococcus were cultivated particularly in HP(-) sample.
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Davis, James J., Fangfang Xia, Ross A. Overbeek, and Gary J. Olsen. "Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes." International Journal of Systematic and Evolutionary Microbiology 63, Pt_7 (July 1, 2013): 2727–41. http://dx.doi.org/10.1099/ijs.0.048983-0.

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The tree of life is paramount for achieving an integrated understanding of microbial evolution and the relationships between physiology, genealogy and genomics. It provides the framework for interpreting environmental sequence data, whether applied to microbial ecology or to human health. However, there remain many instances where there is ambiguity in our understanding of the phylogeny of major lineages, and/or confounding nomenclature. Here we apply recent genomic sequence data to examine the evolutionary history of members of the classes Mollicutes (phylum Tenericutes ) and Erysipelotrichia (phylum Firmicutes ). Consistent with previous analyses, we find evidence of a specific relationship between them in molecular phylogenies and signatures of the 16S rRNA, 23S rRNA, ribosomal proteins and aminoacyl-tRNA synthetase proteins. Furthermore, by mapping functions over the phylogenetic tree we find that the erysipelotrichia lineages are involved in various stages of genomic reduction, having lost (often repeatedly) a variety of metabolic functions and the ability to form endospores. Although molecular phylogeny has driven numerous taxonomic revisions, we find it puzzling that the most recent taxonomic revision of the phyla Firmicutes and Tenericutes has further separated them into distinct phyla, rather than reflecting their common roots.
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Khlestkin, V. K., M. N. Lockachuk, O. A. Savkina, L. I. Kuznetsova, E. N. Pavlovskaya, and O. I. Parakhina. "Taxonomic structure of bacterial communities in sourdoughs of spontaneous fermentation." Vavilov Journal of Genetics and Breeding 26, no. 4 (July 7, 2022): 385–93. http://dx.doi.org/10.18699/vjgb-22-47.

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The article is devoted to the study of the microbiome of spontaneously fermented sourdoughs. The aim of the work was to study the influence of the technological parameters of sourdough propagations on the taxonomic structure of the microbiome of spontaneously fermented sourdoughs. Two spontaneously fermented sourdoughs were studied: dense rye sourdough and liquid rye sourdough, both prepared using the same batch of peeled rye flour. To study the taxonomic structure of the sourdough microbiome in dynamics, the method of high-throughput sequencing of 16S rRNA gene fragments of microorganisms was used. It was shown that the technological parameters of sourdough (humidity, temperature) do not affect the taxonomic composition of the microbiome of dense rye or liquid rye sourdough at the phylum/class/genus level. It was found that during the first three days of propagations, bacteria from the phyla Proteobacteria and Firmicutes dominated in the microbial community. In the phylum Proteobacteria, microorganisms from the order Enterobacterales took a large share, which persisted for three days of backslopping. The phylum Firmicutes was represented by lactic acid bacteria of the genera Weissella, Lactobacillus, Leuconostoc, Pediococcus, Lactococcus. It was established by classical microbiological methods that after a day of fermentation, the number of lactic acid bacteria cells was significantly higher in liquid rye sourdough compared to dense one. However, with further propagation of sourdoughs, the number of cells was comparable, while significant changes occurred at the level of genera and species. It was shown that as the relative number of lactic acid bacteria of the genus Lactobacillus increased, a gradual displacement of the coccal forms of Lactococcus, Leuconostoc, Weissella, Pediococcus happened. With further propagation of sourdough after 10 days, the position of the dominant groups of bacteria was occupied by representatives of the phylum Firmicutes, lactic acid bacteria of the genus Lactobacillus. The influence of the mode and parameters of the sourdough on the species composition of lactobacilli, which demonstrated a low bacterial diversity, is shown. In the first three days of propagations, lactobacilli L. curvatus, L. brevis, and Lactiplantibacillus sp. dominated in both sourdoughs. After a month of backslopping, Fructilactobacillus sanfranciscensis and Companilactobacillus sp. dominated in dense rye sourdough, and L. pontis dominated in liquid rye sourdough.
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Rodriguez-Mora, Maria J., Virginia P. Edgcomb, Craig Taylor, Mary I. Scranton, Gordon T. Taylor, and Andrei Y. Chistoserdov. "The Diversity of Sulfide Oxidation and Sulfate Reduction Genes Expressed by the Bacterial Communities of the Cariaco Basin, Venezuela." Open Microbiology Journal 10, no. 1 (August 31, 2016): 140–49. http://dx.doi.org/10.2174/1874285801610010140.

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Qualitative expression of dissimilative sulfite reductase (dsrA), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. Neither of the two could be amplified from mRNA retrieved with Niskin bottles but were amplified from mRNA retrieved by the Deep SID. Thesqrandsqr-like genes retrieved from the Cariaco Basin were related to thesqrgenes from aBradyrhizobiumsp.,Methylomicrobium alcaliphilum,Sulfurovumsp. NBC37-1,Sulfurimonas autotrophica, Thiorhodospira sibiricaandChlorobium tepidum. ThedsrAgene sequences obtained from the redoxcline of the Cariaco Basin belonged to chemoorganotrophic and chemoautotrophic sulfate and sulfur reducers belonging to the class Deltaproteobacteria (phylum Proteobacteria) and the order Clostridiales (phylum Firmicutes).
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Zhang, Guolin, Xingbiao Chu, Hanyang Zhu, Dongsheng Zou, Longcheng Li, and Linsen Du. "The Response of Soil Nutrients and Microbial Community Structures in Long-Term Tea Plantations and Diverse Agroforestry Intercropping Systems." Sustainability 13, no. 14 (July 13, 2021): 7799. http://dx.doi.org/10.3390/su13147799.

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During tea cultivation, diverse agroforestry is an important and established intercropping measure, with most studies concentrating on ecological service provision and economic returns. However, the response of soil nutrients and microbial community structures in long-term tea plantations with diverse agroforestry intercropping systems is poorly understood. In the present field study (2015), three intercropping agroforestry-tea patterns (Osmanthus-Tea (OT), Michelia-Tea (MT), Osmanthus-Michelia-Tea (OMT)) along with a study control (C) were examined in terms of these two knowledge gaps. Results showed that, in terms of tea cultivation, the OMT system is more suitable than the OT and MT systems. The OMT system significantly increased the total nitrogen (TN, 16.4%), total potassium (TK, 10.5%), available nitrogen (AN, 14.2%), available phosphorus (AP, 26.7%) and soil organic matter (SOM, 28.9%). The OMT system increased phylum Firmicutes and Bacteroidetes abundance by 35.8% and 9.6%. In addition, the OMT system enhanced the abundance of class Bacteroidia (99.5%), Erysipelotrichia (96.9%), Clostridia (93.5%) and Actinobacteria (19.6%), respectively. In general, the phylum bacteria Proteobacteria, Firmicutes, Actinobacteria accounted for the largest proportion of bacteria in all three intercropping systems. In this study, the abundance of Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were positively correlated with AN, SOM and TP. The results of the present study will help to develop a better understanding of the benefits imposed by different agroforestry intercropping systems on nutrient dynamics and microbial structural diversity during tea cultivation.
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Agwunobi, Desmond Onyeka, Joshua Kamani, Hongyuan Zheng, Lida Guo, Zhijun Yu, and Jingze Liu. "Bacterial Diversity in Rhipicephalus sanguineus (Acari: Ixodidae) from Two States in Nigeria." Journal of Entomological Science 56, no. 2 (April 1, 2021): 256–71. http://dx.doi.org/10.18474/0749-8004-56.2.256.

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Abstract Rhipicephalus sanguineus (Latreille) is the most widely distributed tick species globally and plays a major role in tick-borne pathogen transmission among canine populations. The microbial community of this tick has not been characterized previously in Nigeria. Thus, in this study, the bacterial diversity in R. sanguineus collected from two states in Nigeria was explored using 16S rRNA high-throughput sequencing (IonS5TM XL sequencing platform). Three hundred genera (although 18 groups belong to unidentified genera) of bacteria belonging to 22 phyla were detected after pooling and sequencing, indicating a diverse bacterial community profile. At the phylum level, Actinobacteria (47.39%) was the most abundant phylum in the Benue state samples, followed by Proteobacteria (43.87%) and Firmicutes (8.21%), whereas Fusobacteria (38.14%) was the most abundant phylum in Plateau state samples, followed by Bacteroidetes (17.57%) and Firmicutes (17.54%). Proteobacteria accounts for 17% of samples from Plateau state. In general, Cetobacterium (35.86%) was the most abundant genus, followed by an unidentified genus under Corynebacteriaceae (29.94%) and Stenotrophomonas (19.52%). Coxiella spp., one common endosymbiont found in various tick species, was present in R. sanguineus. This study provides a baseline of knowledge of the bacterial microbiome of R. sanguineus in Nigeria. Nonpathogenic bacteria species were prevalent, and not much is known about their role. Thus, their composition, functional, and ecologic implications merit further investigation because this will aid in the subsequent management of ticks and tick-borne diseases.
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Han, Haiyin, Yingjie Sun, Yekai Fan, Hui Zhang, Junqi Yang, Runqing Chi, Yahui Gao, et al. "Microbial Diversity and Community Composition of Duodenum Microbiota of High and Low Egg-Yielding Taihang Chickens Identified Using 16S rRNA Amplicon Sequencing." Life 12, no. 8 (August 18, 2022): 1262. http://dx.doi.org/10.3390/life12081262.

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The duodenum is an important digestive organ for poultry and houses a variety of microbes that help chickens to enhance nutrient absorption and improve production. To evaluate the characteristic of gut microbiome, duodenum content samples from 42-week-old native Taihang chickens with high (H) and low (L) egg-yielding were collected for 16S rRNA amplicon sequencing analysis. Consequently, 1,361,341 sequences were clustered into 2055 OTUs, with percentages of affiliation of 96.50 and 57.30% at phylum and genus levels. Firmicutes, Proteobacteria, Cyanobacteria and Bacteroidetes were the dominant phylum, with a lower ratio of Firmicutes/Bacteroidetes in H group than in L group (p < 0.05). At genus level, overrepresentation of Bacteroides, Faecalibacterim, and Enterococcus and underrepresentation of Romboutsia were found in H group. No significant difference in overall diversity of microbiota was observed between two groups. LEFSe analysis revealed Enterococcus was significantly enriched in H group. Importantly, Enterococcus and Lactobacillus were negatively correlated. Functional prediction analysis showed the proportion of microbiota involved in the metabolism process was the highest and enriched in H group. Differences in microbiota composition between the two groups, which may be related to intestinal function difference, also provide promising biomarkers for improving laying hen production.
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Nakajima, Hanako, Fumie Takewaki, Yoshitaka Hashimoto, Shizuo Kajiyama, Saori Majima, Hiroshi Okada, Takafumi Senmaru, et al. "The Effects of Metformin on the Gut Microbiota of Patients with Type 2 Diabetes: A Two-Center, Quasi-Experimental Study." Life 10, no. 9 (September 11, 2020): 195. http://dx.doi.org/10.3390/life10090195.

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Metformin is reported to affect human gut microbiota; however, the nature of this association in Japanese patients with type 2 diabetes mellitus (T2DM) is unknown. We enrolled 31 patients with T2DM who took metformin for the first time in this study. We compared them before and after four weeks of taking metformin. Fecal samples were collected and 16S rDNA sequences were performed to identify the gut microbiota. Blood samples and Gastrointestinal Symptom Rating Scale (GSRS) questionnaire results, denoting gastro-intestinal symptoms, were also collected. In the whole-group analysis, no significant differences were found at the phylum level. In a subgroup of 21 patients that excluding those using medications affecting gut microbiota, there was a significant decrease of the phylum Firmicutes (p = 0.042) and of the ratio of the Firmicutes and Bacteroidetes abundances (p = 0.04) after taking metformin. Changes in abdominal pain (r = −0.56, p = 0.008) and regurgitation (r = −0.53, p = 0.01) were associated with Parabacteroides. Despite there being no direct association with abdominal symptoms, our study revealed that the composition of gut microbiota in Japanese individuals with T2DM partially changed after starting metformin.
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Suleiman, Majda K., Kingsley Dixon, Lucy Commander, Paul Nevill, Ali M. Quoreshi, Narayana R. Bhat, Anitha J. Manuvel, and Mini T. Sivadasan. "Evaluating the diversity and composition of bacterial communities associated withVachellia pachyceras— the only existing native tree species in the Kuwait desert." Canadian Journal of Microbiology 65, no. 3 (March 2019): 235–51. http://dx.doi.org/10.1139/cjm-2018-0421.

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We investigated the diversity and composition of bacterial communities in rhizospheric and non-rhizospheric bulk soils as well as root nodule bacterial communities of Vachellia pachyceras — the only native tree species existing in the Kuwait desert. Community fingerprinting comparisons and 16S rDNA sequence identifications were used for characterization of the bacterial population using specific primers. The bacterial characterization of soil samples revealed four major phyla: Acidobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. In situ (desert) samples of both rhizospheric and non-rhizospheric bulk soil were dominated by the bacterial phyla Firmicutes and Bacteroidetes, whereas the phylum Betaproteobacteria was present only in non-rhizospheric bulk soil. Ex situ (nursery growing condition) V. pachyceras resulted in restricted bacterial communities dominated by members of a single phylum, Bacteroidetes. Results indicated that the soil organic matter and rhizospheric environments might drive the bacterial community. Despite harsh climatic conditions, data demonstrated that V. pachyceras roots harbor endophytic bacterial populations. Our findings on bacterial community composition and structure have major significance for evaluating how Kuwait’s extreme climatic conditions affect bacterial communities. The baseline data obtained in this study will be useful and assist in formulating strategies in ecological restoration programs, including the application of inoculation technologies.
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Verma, Pankaj, Chi Nam Seong, Prashant Kumar Pandey, Ramesh Ramchandra Bhonde, Cathrin Spröer, Manfred Rohde, and Yogesh Shreepad Shouche. "Bhargavaea indica sp. nov., a member of the phylum Firmicutes, isolated from Arabian Sea sediment." Journal of Microbiology 51, no. 1 (February 2013): 36–42. http://dx.doi.org/10.1007/s12275-013-2488-z.

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Fan, Li, Weiping Zhao, Wendan Feng, Ping Mo, Yunlin Zhao, Guiyan Yang, and Zhenggang Xu. "Insight into the Characteristics of Soil Microbial Diversity during the Ecological Restoration of Mines: A Case Study in Dabaoshan Mining Area, China." Sustainability 13, no. 21 (October 22, 2021): 11684. http://dx.doi.org/10.3390/su132111684.

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Soil microorganisms play an important role in regulating a variety of ecological functions. In recent years, the research on ecological restoration after mining has made people more aware of the importance of microbial diversity to ecosystem restoration. The present study investigated the effect of ecological restoration on microbial community structure and its relationship with soil physicochemical properties in the Dabaoshan mining area, China. High throughput sequencing technology was used to analyze and compare the microbial community composition of three types of soil (undamaged area, unrestoration area, and ecological restoration area). The contents of organic carbon, total nitrogen, and total phosphorus were 2.38–12.97 g/kg, 0.39–1.62 g/kg, and 0.99–1.51 g/kg, respectively. In different soil states, undamaged area and ecological restoration area were significantly higher than those in unrestoration area. The results showed that the structure of soil microbial community was significantly correlated with soil physicochemical properties, and formations in the repaired and unrepaired soils were different. Operational Taxonomic Unit (OTU) cluster analysis and diversity index analysis showed that soil microbial community changed at phylum and genus levels. The results showed that at the phylum level, all soil samples contained Firmicutes, Proteobacteria, and actinobacteria. Firmicutes and Proteobacteria of the ecological restoration area (ER1, ER2) were the highest in relative abundance compared with other samples, accounting for more than 45%. Proteobacteria and Acidobacteria were the dominant phylum in the undamaged area (UD), accounting for 32.7% and 22.3%, respectively. It can be seen that soil restoration produced a new dominant population, and Proteobacteria showed an absolute competitive advantage in the mining soil.
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Song, Fengcheng, Yishu Xu, Peng Peng, Hongxu Li, Ranxi Zheng, Haolin Zhang, Yingying Han, Qiang Weng, and Zhengrong Yuan. "Seasonal Changes in the Structure and Function of Gut Microbiota in the Muskrat (Ondatra zibethicus)." Metabolites 13, no. 2 (February 9, 2023): 248. http://dx.doi.org/10.3390/metabo13020248.

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The gut microbiota plays a crucial role in the nutrition, metabolism, and immune function of the host animal. The muskrat (Ondatra zibethicus) is a typical seasonal breeding animal. The present study performed a metagenomic analysis of cecum contents from muskrats in the breeding and non-breeding seasons. The results indicated that the breeding muskrats and non-breeding muskrats differed in gut microbiota structure and function. During the breeding season, the relative abundance of phylum Bacteroidetes, genus Prevotella, and genus Alistipes increased, while the relative abundance of phylum Firmicutes and phylum Actinobacteria decreased. The muskrat gut microbiota was enriched in the metabolism-related pathways, especially amino acid and vitamin metabolism, and genetically related metabolites in the breeding season. We presumed that the muskrat gut microbiota might seasonally change to secure reproductive activity and satisfy the metabolic demands of different seasons. This study could explore potential mechanisms by which gut microbiota affects reproduction. Moreover, this study may provide a new theoretical basis for the management of muskrat captive breeding.
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Martinez-Steele, Laura, Chris G. Lowe, Mark S. Okihiro, and Renaud Berlemont. "Draft Genome Sequences of Nine New Carnobacterium maltaromaticum Strains Isolated from Diseased Sharks." Genome Announcements 6, no. 18 (May 3, 2018): e00354-18. http://dx.doi.org/10.1128/genomea.00354-18.

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ABSTRACT Here, we report the draft genome sequences of 9 strains of Carnobacterium maltaromaticum (SK_LD1 to SK_LD3 and SK_AV1 to SK_AV6), a member of the Carnobacteriaceae family (phylum Firmicutes). These strains were isolated from the brain and the inner ear of three diseased thresher sharks and two diseased salmon sharks. The genome assembly resulted in an average of 3,306,205.9 ± 29,143.9 bp and 3,085 ± 32.67 coding DNA sequences (CDS).
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Chen, Qu, Dan Hu, Xiaoting Wu, Yuyan Feng, and Yingdong Ni. "Dietary γ-Aminobutyric Acid Supplementation Inhibits High-Fat Diet-Induced Hepatic Steatosis via Modulating Gut Microbiota in Broilers." Microorganisms 10, no. 7 (June 24, 2022): 1281. http://dx.doi.org/10.3390/microorganisms10071281.

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The present study aims to investigate the effect of γ-aminobutyric acid (GABA) on liver lipid metabolism and on AA broilers. Broilers were divided into three groups and fed with low-fat diets, high-fat diets, and high-fat diets supplemented with GABA. Results showed that GABA supplementation decreased the level of triglyceride (TG) in the serum and liver of broilers fed high-fat diets, accompanied by up-regulated mRNA expression of genes related to lipolysis and β-oxidation in the liver (p < 0.05). Furthermore, GABA supplementation increased liver antioxidant capacity, accompanied by up-regulated mRNA expression of antioxidant genes (p < 0.05). 16S rRNA gene sequencing showed that GABA improved high-fat diet-induced dysbiosis of gut microbiota, increased the relative abundance of Bacteroidetes phylum and Barnesiella genus, and decreased the relative abundance of Firmicutes phylum and Ruminococcus_torques_group and Romboutsia genus (p < 0.05). Moreover, GABA supplementation promoted the production of propionic acid and butyric acid in cecal contents. Correlation analysis further suggested the ratio of Firmicutes/Bacteroidetes negatively correlated with hepatic TG content, and positively correlated with cecal short chain fatty acids content (r > 0.6, p < 0.01). Together, these data suggest that GABA supplementation can inhibit hepatic TG deposition and steatosis via regulating gut microbiota in broilers.
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Guo, Yan, Zhi-Ping Huang, Chao-Qian Liu, Lin Qi, Yuan Sheng, and Da-Jin Zou. "Modulation of the gut microbiome: a systematic review of the effect of bariatric surgery." European Journal of Endocrinology 178, no. 1 (January 2018): 43–56. http://dx.doi.org/10.1530/eje-17-0403.

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Objective Bariatric surgery is recommended for patients with obesity and type 2 diabetes. Recent evidence suggested a strong connection between gut microbiota and bariatric surgery. Design Systematic review. Methods The PubMed and OVID EMBASE were used, and articles concerning bariatric surgery and gut microbiota were screened. The main outcome measures were alterations of gut microbiota after bariatric surgery and correlations between gut microbiota and host metabolism. We applied the system of evidence level to evaluate the alteration of microbiota. Modulation of short-chain fatty acid and gut genetic content was also investigated. Results Totally 12 animal experiments and 9 clinical studies were included. Based on strong evidence, 4 phyla (Bacteroidetes, Fusobacteria, Verrucomicrobia and Proteobacteria) increased after surgery; within the phylum Firmicutes, Lactobacillales and Enterococcus increased; and within the phylum Proteobacteria, Gammaproteobacteria, Enterobacteriales Enterobacteriaceae and several genera and species increased. Decreased microbial groups were Firmicutes, Clostridiales, Clostridiaceae, Blautia and Dorea. However, the change in microbial diversity is still under debate. Faecalibacterium prausnitzii, Lactobacillus and Coprococcus comes are implicated in many of the outcomes, including body composition and glucose homeostasis. Conclusions There is strong evidence to support a considerable alteration of the gut microbiome after bariatric surgery. Deeper investigations are required to confirm the mechanisms that link the gut microbiome and metabolic alterations in human metabolism.
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Watanabe, Miho, Hisaya Kojima, and Manabu Fukui. "Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes." International Journal of Systematic and Evolutionary Microbiology 65, Pt_8 (August 1, 2015): 2378–84. http://dx.doi.org/10.1099/ijs.0.000267.

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A novel facultatively anaerobic bacterium, strain HC45T, was isolated from sediment of a brackish meromictic lake in Japan, Lake Harutori. Cells were pleomorphic, and filamentous bodies were 5–100 μm in length. For growth, the optimum pH was 7.0 and the optimum temperature was 45–50 °C. The G+C content of the genomic DNA was 71 mol%. iso-C15 : 0 and anteiso-C15 : 0 were the major components in the cellular fatty acid profile. The predominant respiratory quinone was MK-7. Strain HC45T shared very low 16S rRNA gene sequence similarity with cultivated strains ( ≤ 85 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was distantly related to members of the family Symbiobacteriaceae and family XVII Incertae Sedis in the class Clostridia, and they formed a cluster separate from canonical species of the phylum Firmicutes. These results indicated that strain HC45T should not be placed in any existing class of the phylum Firmicutes. On the basis of phylogenetic and phenotypic characterization, Limnochorda pilosa gen. nov., sp. nov. is proposed with HC45T ( = NBRC 110152T = DSM 28787T) as the type strain, as the first representative of novel taxa, Limnochordales ord. nov., Limnochordaceae fam. nov. in Limnochordia classis. nov.
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Sobhonslidsuk, Abhasnee, Suwannee Chanprasertyothin, Tanjitti Pongrujikorn, Piyaporn Kaewduang, Kwannapa Promson, Supanna Petraksa, and Boonsong Ongphiphadhanakul. "The Association of Gut Microbiota with Nonalcoholic Steatohepatitis in Thais." BioMed Research International 2018 (2018): 1–8. http://dx.doi.org/10.1155/2018/9340316.

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Objectives. Nonalcoholic steatohepatitis (NASH) can progress to advanced fibrosis; the link between intestinal bacterial overgrowth and NASH has been proposed. Gut microbiota may promote inflammation and provoke disease progression. We evaluated gut microbiota pattern in NASH and its influencing factors. Methods. A case-controlled study with sixteen NASH and eight control subjects was done. We performed DNA extraction from stool samples and bacterial 16S rRNA sequencing using MiSeq™. The sequences were clustered into operational taxonomic units using Quantitative Insights Into Microbial Ecology software. We calculated relative abundances, determined alpha diversity, obtained beta diversity by principal coordinate analysis, and conducted the partial least-squares regression model. Results. The relative abundance of Bacteroidetes tended to be higher in NASH group. The Bacteroidetes/Firmicutes (B/F) ratio was significantly elevated in NASH patients. The pattern of gut microbiota in NASH was clearly separated from that of control subjects. Factors influencing the separation of NASH from control subjects were age, diabetes, body mass index, Bacteroidetes phylum, metformin, Actinobacteria, Verrucomicrobia, Thermotogae, and Caldithrix and Bacteroidetes/Firmicutes ratio. Conclusions. Bacteroidetes phylum (Bacteroides and Prevotella genus) is abundant in NASH subjects, who exhibited an elevated B/F ratio. NASH patients showed a specific pattern of gut microbiota independent of diabetes or metformin use.
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Amin, Mariam E., Marwa Azab, Amro Hanora, Khaled Atwa, and Sarah Shabayek. "Compositional Changes in the Vaginal Bacterial Microbiome of Healthy Pregnant Women across the Three Gestational Trimesters in Ismailia, Egypt." Microorganisms 11, no. 1 (January 5, 2023): 139. http://dx.doi.org/10.3390/microorganisms11010139.

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The composition of the vaginal microbiome may lead to adverse pregnancy outcomes. Normal pregnancy is associated with changes in the vaginal bacterial community composition, which tend to be more enriched with one or two Lactobacillus species promoting a healthy vagina and favorable birth outcomes. The aim of the current study was to determine compositional changes in the healthy vaginal microbiome composition during the three trimesters of pregnancy in Ismailia, Egypt using Illumina MiSeq sequencing of the V3–V4 region of the 16S rRNA. The phylum Firmicutes and the genus Lactobacillus dominated across the three trimesters of pregnancy. L. iners was the most abundant species. However, L. coleohominis and L. reuteri represented the least dominant vaginal lactobacilli. Core microbiome analyses showed the Lactobacillus genus and L. iners species to have the highest prevalence in all the samples of our study groups. The phylum Firmicutes was found to be negatively correlated with almost all other vaginal phyla during pregnancy. Likewise, a negative correlation between Lactobacillus and almost all other genera was detected, including significant negative correlations with Dialister and Prevotella. Furthermore, negative correlations of L. iners were detected with almost all other species, including a significant negative correlation with L. helveticus, G. vaginalis, S. anginosus, and S. agalactiae.
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D'Auria, G., J. C. Galan, M. Rodriguez-Alcayna, A. Moya, F. Baquero, and A. Latorre. "Complete Genome Sequence of Acidaminococcus intestini RYC-MR95, a Gram-Negative Bacterium from the Phylum Firmicutes." Journal of Bacteriology 193, no. 24 (November 28, 2011): 7008–9. http://dx.doi.org/10.1128/jb.06301-11.

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Liu, Tian, and Yi Hu. "Intestinal microbiota to predict risk for immune-related diarrhea in patients with lung cancer patients." Journal of Clinical Oncology 36, no. 5_suppl (February 10, 2018): 132. http://dx.doi.org/10.1200/jco.2018.36.5_suppl.132.

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132 Background: Anti-programmed cell death 1 (PD-1) inhibitors, which enhance cellular immunity via blockade of PD-1, represent an effective option for the treatment of lung cancer and have shown some impressive efficacy. However, the inhibitors can also result in immune-related adverse events, such as immune-related diarrhea. Researches have shown that intestinal microbiota plays a vital role in gastrointestinal dysregulation. Whereas, the relationship between PD-1 inhibitors and immune-related diarrhea is still elusive. In our study, we aim to identify the correlation of intestinal microbiota and immune-related diarrhea, and hope to find specific bacteria as potential biomarkers of immune-related diarrhea. Methods: Twenty-six lung cancer patients who were treated with PD-1 inhibitors from 301 hospital were enrolled for retrospective analysis. And the fecal samples were obtained from patients before the first dose of PD-1 inhibitor. Based on whether they develop diarrhea or not, the patients were subgroup into progressed to diarrhea(PtD) group and diarrhea-free(D-F) group. Immune-related diarrhea was graded according to the National Cancer Institute Common Toxicity Criteria (CTC, version 4.0). And 16S rRNA sequencing was used to profile fecal bacterial composition. Results: There was no significant difference in baseline characteristics, such as microbial richness between PtD group and D-F group (P > 0.05). However, At the phylum level, Bacteroidetes were richer in D-F group, while Firmicutes were poorer, than that in PtD group. At the genus level, two families of the Bacteroidetes phylum ( Bacteroides and Parabacteroides) and a family of the Firmicutes phylum (Phascolarctobacterium) were more abundant in D-F group. Veillonella from Proteobacteria phylum was lower in D-F group than that in PtD group (all P < 0.05). Conclusions: Our study indicates that microbiota variation probably participates in the onset of immune-related diarrhea. Identifying these biomarkers may help us to diagnose the side effect earlier, and provides a novel treatment for immune-related diarrhea due to PD-1 inhibitors.
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Nakajima, Akira, Alexis Vogelzang, Mikako Maruya, Michio Miyajima, Megumi Murata, Aoi Son, Tomomi Kuwahara, et al. "IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria." Journal of Experimental Medicine 215, no. 8 (July 24, 2018): 2019–34. http://dx.doi.org/10.1084/jem.20180427.

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Immunoglobulin A (IgA) promotes health by regulating the composition and function of gut microbiota, but the molecular requirements for such homeostatic IgA function remain unknown. We found that a heavily glycosylated monoclonal IgA recognizing ovalbumin coats Bacteroides thetaiotaomicron (B. theta), a prominent gut symbiont of the phylum Bacteroidetes. In vivo, IgA alters the expression of polysaccharide utilization loci (PUL), including a functionally uncharacterized molecular family provisionally named Mucus-Associated Functional Factor (MAFF). In both mice and humans, MAFF is detected predominantly in mucus-resident bacteria, and its expression requires the presence of complex microbiota. Expression of the MAFF system facilitates symbiosis with other members of the phylum Firmicutes and promotes protection from a chemically induced model of colitis. Our data reveal a novel mechanism by which IgA promotes symbiosis and colonic homeostasis.
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Cordero-Ramírez, Jesús Damián, Alejandro Miguel Figueroa-López, Juan Carlos Martínez-Álvarez, Melina López-Meyer, Claudia Castro-Martínez, Juan José Morales-Aguilar, and Ignacio Eduardo Maldonado-Mendoza. "Culturable bacteria of the maize rhizosphere: conserving Mexican potential biotechnological resources." Revista Mexicana de Biodiversidad 93 (September 30, 2022): e933561. http://dx.doi.org/10.22201/ib.20078706e.2022.93.3561.

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Rhizospheric microbiota diversity of crops in agroecosystems is understudied in Mexico and worldwide. The aim of the present work was to explore the diversity of culturable bacteria in maize fields. A bacterial collection consisting of 11,520 purified isolates was created from the rhizosphere of maize plants. Genomic DNA was obtained from each isolate and a region of 16S rDNA was sequenced. The 16S rDNA amplicon sequences were analyzed and grouped into Operational Taxonomic Units (OTUs), allowing the assemblage of 7,077 bacterial isolates into 185 non-singleton OTUs. OTUs belonged to 19 bacterial genera within Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes Phyla; with Firmicutes as the richest Phylum comprising 146 OTUs and 6 genera, and being Bacillus the richest genus. The soil core-community of 28 OTUs belonging to Firmicutes and 1 OTU from Proteobacteria was identified. The work discusses the role that the different bacterial populations identified within the maize rhizosphere may play, their potential use for biotechnological purposes, and the importance of conservation of microbiological resources using bacterial collections.
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