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Composition and Diversity of Human Oral Microbiome
Published in Chaminda Jayampath Seneviratne, Microbial Biofilms, 2017
Preethi Balan, Chaminda Jayampath Seneviratne and Wim Crielaard
The compilation of HOMD has revealed that the human oral microbiome comprises approximately 700 bacterial species, including officially named and unnamed as well as culturable and non-culturable phylotypes. The oral microbiome is composed mainly of bacteria which belong to well-known phyla – Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Fusobacteria, Tenericutes and Chylamydiae – as well as the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1 and WPS-2 [44]. The majority of oral representatives (about 96%) permeated into the phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Spirochaetes and Fusobacteria (as accessed www.homd.org on 15 June 2016) (Figure 4.3).
Enhanced removal of antibiotics using Eichhornia crassipes root biomass in an aerobic hollow-fiber membrane bioreactor
Published in Biofouling, 2022
Sevcan Aydin, Duygu Nur Arabacı, Aiyoub Shahi, Hadi Fakhri, Suleyman Ovez
In the phylogenetic tree of sludge samples, bacterial communities were divided into two groups, based on both weighted and unweighted Unifrac distance. Based on weighted Unifrac distance, bacterial diversity in the C1 and C2 reactors were markedly different from the EC reactor; in other words, the bioreactor with WHRB showed different bacterial diversity from other bioreactors, while, based on unweighted Unifrac distance, the C1 and EC samples showed different bacterial diversity from the C2 sample. In both the weighted and unweighted Unifrac, the dominant bacterial phyla in the three samples were highly similar, including Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Nitrospirae, Spirochaetes, Acidobacteria, Actinobacteria, Chlorobi, and Saccharibacteria. The results also indicated that Proteobacteria followed by Bacteroidetes were the two phyla with the highest relative abundance in the C1 and EC reactors based on weighted Unifrac and in all three sludge samples based on unweighted Unifrac analysis. In the C2 reactor the relative abundance of Firmicutes was higher than Bacteroidetes, however, the Proteobacteria had the highest relative abundance also.
A double-blind, 377-subject randomized study identifies Ruminococcus, Coprococcus, Christensenella, and Collinsella as long-term potential key players in the modulation of the gut microbiome of lactose intolerant individuals by galacto-oligosaccharides
Published in Gut Microbes, 2021
M. A. Azcarate-Peril, J. Roach, A. Marsh, William D. Chey, William J. Sandborn, Andrew J. Ritter, Dennis A. Savaiano, T. R. Klaenhammer
Sequencing of 16S rRNA amplicons targeting the variable region 4 of the ribosomal gene was performed on samples corresponding to treatment groups: (1) Placebo, (2) GOS Low, (3) GOS High (N = 1,332). Amplicon sequencing yielded a total of 254,386,079 sequences (188,994 mean reads per sample). Overall, sequencing data assigned the majority of Operational Taxonomic Units (OTUs) to the phyla Firmicutes averaging 38.9 ± 22.4% per treatment group and time, Bacteroidetes (36.5 ± 18.2%), Proteobacteria (4.1 ± 1.3%), Verrucomicrobia (3.3% ± 2%), and Actinobacteria (2.3% ± 1.7%). The Archaea Euryarchaeota and the phylum Tenericutes were represented at 0.21 ± 0.24, and 0.13 ± 0.11, respectively. The phyla Cyanobacteria, Fusobacteria, OD1, Synergistetes, TM7, Lentisphaerae, Elusimicrobia, Spirochetes were identified in a range from 0.003% to 0.07%, and the phyla [Thermi], Chlorobi, Deferribacteres, Planctomycetes, Armatimonadetes, SR1, Crenarchaeota (Archaea), and Aquificae had the lowest representation (from 7.02 × 10−7 to 2.4 × 10−5%) (Figure 1a).
Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses
Published in Biofouling, 2018
Wei Ding, Chunfeng Ma, Weipeng Zhang, Hoyin Chiang, Chunkit Tam, Ying Xu, Guangzhao Zhang, Pei-Yuan Qian
To understand the molecular mechanisms of how butenolide prevents biofilm development and the interaction between this chemical and microbes, three types of biofilms, including biofilms developed on 5 wt% butebolide, 5 wt% DCOIT and the control panel (only coated with the polymer) were selected for metatranscriptomic analysis. Metatranscriptomics can reveal both the taxonomic composition and active functions of complex microbial communities. A total of 10.76 Gb of metatranscriptomic sequences were generated (two biological replicates for each type of biofilm and in total six metatranscriptomes), and the sequence information is summarized in Table 3. It was hypothesized that, given the different anti-biofilm properties of the three types of panels, variances in the biofilm compositions should be observed. MEGAN analysis was performed to determine the biofilm community structures, which were first observed at the phylum level (Proteobacteria were classified down to classes). As a result, 16 microbial taxa were detected with an abundance > 1% in at least one biofilm (Figure 6). Statistical analysis suggested seven of the 16 groups with significant changes in relative abundance (one-way ANOVA running on proportion data, p < 0.01 and the F values and p values for the comparisons at phylum level are given), including Bacteroidetes/Chlorobi (F = 83.01, p = 0.002), Chloroflexi (F = 47.21, p = 0.005), Gammaproteobacteria (F = 54.80, p = 0.004), Cyanobacteria (F = 345.96, p = 0.000), Actinobacteria (F = 33.28, p = 0.009), Chlamydiae/Verrucomicrobia (F = 60.06, p = 0.004), and Fibrobacteres/Acidobacteria (F = 650.25, p = 0). The microbes were then classified down to the genus level. In total 25 genera were identified with an abundance > 1% in at least one biofilm (Figure 7) and 13 showed significant changes (one-way ANOVA, p < 0.01) between the three biofilm groups, including Bacteriovorax, Alteromonas, Rhodobacteraceae, Acetobacteraceae, Azospirillum, Thalassospira, Alphaproteobacterium HIMB59, Gilvimarinus, Parvibaculum, Cycloclasticus, Beggiatoa, Phaeospirillum and Bacillus.