Deciphering Diversity Indices for a Better Understanding of Microbial Communities

Kim, Bo Ra; Shin, Jiwon; Guevarra, Robin B.; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard E.

doi:10.4014/jmb.1709.09027

Cited by 729 publications

(469 citation statements)

References 30 publications

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Section: Effects On Bacterial and Fungal Diversitysupporting

confidence: 83%

“…An increase in the Shannon's diversity index during ensiling and aerobic exposure corresponded to an increase in bacterial OTUs, a relationship that has been reported by others (Kim et al, 2017) although bacterial species composition did vary between treatments, bacterial diversity was similar for fresh forage, terminal and aerobically exposed barley silages across treatments.…”

Section: Effects On Bacterial and Fungal Diversitysupporting

confidence: 81%

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Impact of field fungal contamination of barley on ensiling properties, nutritional quality and the microbiome of barley silage

Nair

Turkington

Blackshaw

et al. 2019

Grass and Forage Science

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Barley varieties of differing fungal disease resistance were grown in triplicate plots at Lacombe and Lethbridge, Alberta with the disease resistant variety (FR) sprayed with a foliar fungicide to maximize differences in field fungal disease. Both varieties were harvested at soft dough and ensiled in minisilos to assess differences in fungal contamination on ensiling properties, nutritional quality, aerobic stability and associated bacterial and fungal microbiomes. Data were analysed as repeated measures with the effect of treatment × time (duration of ensiling or aerobic exposure) included in the model. The percentage leaf area diseased by net form net blotch was higher (p < 0.05) in the untreated barley cv. Sundre (UN, 59.1% leaf area affected at Lacombe and 25.2% at Lethbridge) than in the FR barley cv. Chigwell (0.7% leaf area affected at Lacombe and 0.1% at Lethbridge). Fungal resistant barley had a lower (p < 0.01) acid and neutral detergent fibre content. Relative abundance of Xanthomonadales was higher (p = 0.02) for FR than UN, while Lactobacillales dominated the bacterial microbiome after 60 day of ensiling in both silages. Bacillales dominated both FR and UN after 21 day of aerobic exposure. Fungal resistant fresh barley forage had a tendency (p = 0.10) for a greater relative abundance of Pleosporales, while UN had higher (p < 0.01) Hypocreales. Mould counts were lower (p = 0.01) for FR than UN after 7 day of ensiling. Fungal resistant barley had minimal influence on the fungal community that contributed to the aerobic deterioration of barley silage.

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Section: Effects On Bacterial and Fungal Diversitysupporting

confidence: 83%

Section: Effects On Bacterial and Fungal Diversitysupporting

confidence: 81%

Impact of field fungal contamination of barley on ensiling properties, nutritional quality and the microbiome of barley silage

Nair

Turkington

Blackshaw

et al. 2019

Grass and Forage Science

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“…Alpha-diversity indices, including Chao1 and Shannon-Weaver diversity indicies, are generally used to compare the differences between microbial communities [21][22][23]. Both saliva and tonsils showed similar richness in microbial communities but the saliva microbiome presented higher evenness than tonsil tissue.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the microbiomic association between tonsil and saliva isolated from Korean children subjected to tonsillectomy using 16S rRNA sequencing: a pilot study

Choi¹,

Park²,

Choi³

et al. 2020

Preprint

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BackgroundOral microbes have the capacity to spread throughout the gastrointestinal system and are significantly associated with multiple diseases. Given that tonsils are located between the oral cavity and laryngoesophagus at the gateway of both alimentary and respiratory tracts, tonsillar tissue may also be affected by both oral (saliva) and alimentary tract microbiota. While several independent reports on oral microbiomes from saliva and tonsils are documented in the literature, limited studies have compared tonsil and saliva microbiota compositions. Here, we analyzed the distribution of the microbial communities in saliva and tonsils of healthy Korean children subjected to tonsillectomy. ResultsIn total, 29 study subjects were enrolled from an initial 45 participants subjected to tonsillectomy owing to hyperplasia over two years. The microbiome profiles of saliva and tonsils were established via 16S rRNA gene sequencing. Based on the Chao1 diversity index, the tonsil group showed higher richness in species, compared to the saliva group. On the other hand, the Shannon index revealed a significantly higher biodiversity value for saliva relative to tonsils. The microbial communities of the two groups were highly similar. The top 10 ranked taxa common to both groups determined based on average relative abundance were as follows: Haemophilus,

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“…Diversity is a measure that estimates the number of different species present in a given microbial community as well as the abundance of each species and is used to quantify the biodiversity of a habitat [36]. Actinobacteria and Firmicutes phyla were chosen because they include the most recognized BV-associated bacteria [17].…”

Section: Discussionmentioning

confidence: 99%

Assessment of vaginal microbiota in Brazilian women with and without bacterial vaginosis and comparison with Nugent score

Oliveira¹,

Diniz²,

Fernandes³

et al. 2018

J Infect Dev Ctries

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Introduction: Bacterial vaginosis (BV) is characterized by the depletion of Lactobacillus spp. population and increase of other species, especially Gardnerella vaginalis and Atopobium vaginae. This study aimed to investigate the vaginal microbiota structure of Brazilian women with and without BV according to Nugent Score and to assess the correlation among Nugent score and the quantification of BV-associated bacteria. Methodology: Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) assay was employed to characterize the vaginal microbiota structure. Quantification of Lactobacillus spp., G. vaginalis, A. vaginae, Mobiluncus sp. and M. hominis were determined by quantitative real-time PCR (qPCR). Results: Clustering by PCR-DGGE revealed differences in microbial structure of the different patient groups. Gardnerella vaginalis, A. vaginae, M. hominis and Mobiluncus sp. were detected at high loads in BV-associated microbiota. Quantification of Lactobacillus spp. showed an inverse correlation with Nugent score while the loads of G. vaginalis, A. vaginae, M. hominis and Mobiluncus sp. indicated a direct correlation with this method. Conclusions: Despite Nugent score is considered the gold standard for BV diagnosis, qPCR stands out as a useful tool for bacteria quantification and an alternative for BV diagnosis. Vaginal microbiota is a complex microbial community although there is a common core among BV and non-BV women. Investigation of vaginal microbiota structure may contribute to the development of tools for diagnosis improvement and therapeutic regimen optimization.

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Deciphering Diversity Indices for a Better Understanding of Microbial Communities

Cited by 729 publications

References 30 publications

Impact of field fungal contamination of barley on ensiling properties, nutritional quality and the microbiome of barley silage

Impact of field fungal contamination of barley on ensiling properties, nutritional quality and the microbiome of barley silage

Characterization of the microbiomic association between tonsil and saliva isolated from Korean children subjected to tonsillectomy using 16S rRNA sequencing: a pilot study

Assessment of vaginal microbiota in Brazilian women with and without bacterial vaginosis and comparison with Nugent score

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