Using Mothur to Determine Bacterial Community Composition and Structure in 16S Ribosomal RNA Datasets

Chappidi, Sruthi; Villa, Erika; Cantarel, Brandi L.

doi:10.1002/cpbi.83

Cited by 40 publications

(16 citation statements)

References 22 publications

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“…Preprocessing of sequences obtained by NGS and extraction of operational taxonomic units (OTUs) was performed using the software mothur (version 1.41.0) [ 20 ]. OTUs of amplicons were designated at 97% sequence similarity.…”

Section: Methodsmentioning

confidence: 99%

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects

et al. 2021

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Recent studies have shown that the gut microbiota modulates the physical and psychological functions of the host through several modes of action. One of them is mediating the production of active neurotransmitters, such as serotonin and gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the central nervous system. Here, we analyzed the relationship between fecal GABA concentration and microbial composition in more than 70 human participants. The gut microbiome composition was analyzed using next-generation sequencing based on 16S ribosomal RNA. High-performance liquid chromatography was used to evaluate the neurotransmitters GABA and glutamate. The GABA level was detected in a broad range (0–330 µg/g feces). The participants’ samples were classified into high (>100 µg/g), medium (10–100 µg/g), and low (<10 µg/g) groups, based on fecal GABA concentration. The results reveal that the microbiome of the high-GABA samples had lower alpha diversity than the other samples. Beta diversity analysis showed significant (p < 0.05) separation between the high-GABA samples and others. Furthermore, we surveyed the abundance of specific GABA producer biomarkers among the microbiomes of tested samples. The family Bifidobacteriaceae exhibited high abundance in the microbiome of the high-GABA group. This study demonstrated that Bifidobacterium abundance was associated with high fecal GABA content in healthy human subjects. These results may aid the development of potential probiotics to improve microbial GABA production, which can support the maintenance of the physical and psychiatric health of the host.

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Section: Methodsmentioning

confidence: 99%

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects

et al. 2021

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“…We used Mothur (version 1.43.0) (Schloss et al, 2009;López-García et al, 2018;Schloss, 2020) to analyze the sequencing data following a standard procedure (mothur.org/wiki/MiSeq_SOP; accessed December 2019) (Kozich et al, 2013) and two extended protocols (Batut et al, 2018;Hiltemann et al, 2018;Chappidi et al, 2019). The raw paired-end reads were merged to 2,838,570 contigs.…”

Section: Sequencing Data Cleaning and Contig Alignmentmentioning

confidence: 99%

The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

Zhang¹,

Qin

Struewing

et al. 2021

Front. Microbiol.

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Microbial drinking water quality in premise plumbing systems (PPSs) strongly affects public health. Bacterial community structure is the essential aspect of microbial water quality. Studies have elucidated the microbial community structure in cold tap water, while the microbial community structures in hot tap and shower water are poorly understood. We sampled cold tap, hot tap, and shower water from a simulated PPS monthly for 16 consecutive months and assessed the bacterial community structures in those samples via high-throughput sequencing of bacterial 16S rRNA genes. The total relative abundance of the top five most abundant phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes) was greater than 90% among the 24 identified phyla. The most abundant families were Burkholderiaceae, Sphingomonadaceae, unclassified Alphaproteobacteria, unclassified Corynebacteriales, and Mycobacteriaceae. A multiple linear regression suggests that the bacterial community diversity increased with water temperature and the age of the simulated PPS, decreased with total chlorine residual concentration, and had a limited seasonal variation. The bacterial community in hot tap water had significantly lower Shannon and Inverse Simpson diversity indices (p < 0.05) and thus a much lower diversity than those in cold tap and shower water. The paradoxical results (i.e., diversity increased with water temperature, but hot tap water bacterial community was less diverse) were presumably because (1) other environmental factors made hot tap water bacterial community less diverse, (2) the diversity of bacterial communities in all types of water samples increased with water temperature, and (3) the first draw samples of hot tap water could have a comparable or even lower temperature than shower water samples and the second draw samples of cold tap water. In both a three-dimensional Non-metric multidimensional scaling ordination plot and a phylogenetic dendrogram, the samples of cold tap and shower water cluster and are separate from hot tap water samples (p < 0.05). In summary, the bacterial community in hot tap water in the simulated PPS had a distinct structure from and a much lower diversity than those in cold tap and shower water.

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“…The tag sequence with the highest abundance was selected as the representative sequence within each OTU. Next, according to the taxonomic database of bacteria and fungi, the OTUs were taxonomically annotated using Mothur (Version v.1.30) [41], and the community structure and species abundance distributions were investigated at different taxonomic levels. Subsequently, the alpha diversity index of the samples was assessed using Mothur software to compare community diversity indices of different samples and summarize ACE, Chao 1, Shannon and Simpson indices at a similarity level of 97%.…”

Section: Sequence Data Processing and Bioinformatics Analysismentioning

confidence: 99%

Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus

Sun

Фан

et al. 2020

BMC Microbiol

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Background The symbiotic bacteria associated with edible fungi are valuable microbial resources worthy of in-depth exploration. It is important to analyze the community structure and succession of symbiotic bacteria in mushrooms. This can assist in the isolation of growth-promoting strains that have an essential relationship with the cultivation cycle as well as the agronomic traits and yields of fruiting bodies. Results In all of the samples from cultivation bags of Hypsizygus marmoreus, 34 bacterial phyla were detected. Firmicutes was the most abundant bacterial phylum (78.85%). The genus Serratia showed an exponential increase in abundance in samples collected from the cultivation bags in the mature period, reaching a peak abundance of 55.74% and the dominant symbiotic flora. The most predominant strain was Serratia odorifera HZSO-1, and its abundance increased with the amount of hyphae of H. marmoreus. Serratia odorifera HZSO-1 could reside in the hyphae of H. marmoreus, promote growth and development, shorten the fruiting cycle by 3–4 days, and further increase the fruiting body yield by 12%. Conclusions This study is a pioneering demonstration of the community structure of the symbiotic microbiota and bacteria-mushroom interaction in the growth and development of edible fungi. This work lays a theoretical foundation to improve the industrial production of mushrooms with symbiotic bacteria as assisting agents.

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Using Mothur to Determine Bacterial Community Composition and Structure in 16S Ribosomal RNA Datasets

Cited by 40 publications

References 22 publications

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects

The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus

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