Genome Diversity of Spore-Forming
            <i>Firmicutes</i>

Galperin, Michael Y.

doi:10.1128/microbiolspectrum.tbs-0015-2012

Cited by 172 publications

(97 citation statements)

References 136 publications

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“…In contrast, the relative proportions of alphaproteobacteria obtained from the fruits at the 0 th , 3 rd and 6 th day after harvest were 48.22, 57.16 and 56.95%, respectively (Table 3). Whilst Bacilli subdivision is a taxonomic Class of bacteria belonging to the phylum Firmicutes (Galperin, 2013), Alphaproteobacteria belong to the phylum Proteobacteria (Madrid et al, 2001).…”

Section: Resultsmentioning

confidence: 99%

Metagenomic analysis of bacterial community associated with postharvest Irvingia species fruit wastes

Etebu¹,

Torunana²,

Parker³

2018

Microbiol Res Int

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The use of culture-dependent methods in studying bacterial community has been proven to be inadequate, and often give misleading results. In this work, metagenomic analysis targeting the 16S ribosomal RNA genes was used to study the diversity and community structure of bacteria associated with postharvest Irvingia fruits. Results showed that Simpson's diversity indices and number of Operational Taxonomic Units were dependent on the storage period (days after harvest, DAH) of fruits. Fresh fruits assessed on the day of harvest (DAH = 0) had a Simpson's diversity index of 0.82, while fruits assessed on the 3 rd and 6 th DAH had diversity indices of 0.69 and 0.72, respectively. Whilst fruits assessed on the day of harvest had 64 OTUs spanning across 7 phyla, 11 Classes, 32 genera with total reads of 23,776, fruits assessed on the 3 rd and 6 th days after harvest had 58 OTUs spanning across 6 phyla, 9 Classes, 30 genera with 20,949 reads and 66 OTUs spanning across 4 phyla, 6 Classes, 33 genera with 30,722 reads, respectively. Results further showed that majority of the OTUs belonged to two phyla -Proteobacteria and Firmicutes, mostly represented by members of Alphaproteobacteria and Bacilli subdivisions respectively. Predominant among these OTUs were sequences belonging to Acetobacter ghanensis (11.94%), A. okinawensis (15.36%), Lactobacillus species (14.90%), L. collinoides (12.35%), L. plantarum (7.11%) and L. vaccinostercus (2.89%). The relative abundance of these microorganisms indicates that fleshy pericarp of Irvingia fruits hitherto treated as wastes could potentially be used as a substrate in food and pharmaceutical industries.

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Section: Resultsmentioning

confidence: 99%

Metagenomic analysis of bacterial community associated with postharvest Irvingia species fruit wastes

Etebu¹,

Torunana²,

Parker³

2018

Microbiol Res Int

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“…In addition, EFF display a large functional diversity and are, therefore, involved in a variety of ecosystem functions (Mandic-Mulec and Prosser, 2011). A multitude of metabolisms can be found among Firmicutes, including aerobic and anaerobic respiration (e.g., sulfate-reduction), acetogenesis, fermentation or phototrophy (Béjà et al, 2002; Logan, 2012; Galperin, 2013). Likewise, different species of Firmicutes display diverse ecological optima.…”

Section: Introductionmentioning

confidence: 99%

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes

et al. 2016

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Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.

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“…Within herbivorous, hindgut-fermenting reptiles, fecal microbiota is dominated by the phylum Firmicutes (Table 12), which consists of species with low molar fractions of guanine and cytosine in their DNA, some with spore-forming capability (Galperin, 2013). OTUs (Hong et al, 2011).…”

Section: Apparent Digestibilitymentioning

confidence: 99%

Physically Effective Fiber Threshold, Apparent Digestibility, and Novel Fecal Microbiome Identification of the Leopard Tortoise (Stigmochelys pardalis)

Modica¹

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Genome Diversity of Spore-Forming Firmicutes

Cited by 172 publications

References 136 publications

Metagenomic analysis of bacterial community associated with postharvest Irvingia species fruit wastes

Metagenomic analysis of bacterial community associated with postharvest Irvingia species fruit wastes

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes

Physically Effective Fiber Threshold, Apparent Digestibility, and Novel Fecal Microbiome Identification of the Leopard Tortoise (Stigmochelys pardalis)

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