Progress in the development of gelling agents for improved culturability of microorganisms

Das, Nilanjan; Tripathi, Naveen; Basu, Srijoni; Bose, Chandra; Maitra, Susmit; Khurana, Sukant

doi:10.3389/fmicb.2015.00698

Cited by 52 publications

(45 citation statements)

References 86 publications

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“…That is, with increasing diversity there is increased redundancy and efficiency of ecosystem processes3940. This has been observed in other microbial studies3541, including those associated with N 2 O emissions42. However, a detailed study linking gaseous emissions (NO, N 2 O and N 2 ), pH and microbial diversity, over soils with varying parent materials and climates, is lacking.…”

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confidence: 92%

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

Samad

Biswas

Bakken

et al. 2016

Sci Rep

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Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.

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mentioning

confidence: 92%

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

Samad

Biswas

Bakken

et al. 2016

Sci Rep

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“…Initial application of PacBio to sequencing full-length fragments suggests that the sequences suffered from a high error rate ( 39 ). To obtain a more direct investigation of rare organisms, microbiologists are developing novel cultivation and single-cell genomic techniques ( 40 – 42 , 48 ). The ability to enrich or select for specific populations using these approaches could limit the need for redundant brute force sequencing.…”

Section: Resultsmentioning

confidence: 99%

Status of the Archaeal and Bacterial Census: an Update

Schloss

Girard

Martin

et al. 2016

mBio

134

110

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A census is typically carried out for people across a range of geographical levels; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the census of full-length 16S rRNA gene sequences is proceeding in the context of recent advances in high-throughput sequencing technologies because full-length sequences are typically used as references for classification of the short sequences generated by newer technologies. Among the 1,411,234 and 53,546 full-length bacterial and archaeal sequences, 94.5% and 95.1% of the bacterial and archaeal sequences, respectively, belonged to operational taxonomic units (OTUs) that have been observed more than once. Although these metrics suggest that the census is approaching completion, 29.2% of the bacterial and 38.5% of the archaeal OTUs have been observed more than once. Thus, there is still considerable diversity to be explored. Unfortunately, the rate of new full-length sequences has been declining, and new sequences are primarily being deposited by a small number of studies. Furthermore, sequences from soil and aquatic environments, which are known to be rich in bacterial diversity, represent only 7.8 and 16.5% of the census, while sequences associated with host-associated environments represent 55.0% of the census. Continued use of traditional approaches and new technologies such as single-cell genomics and short-read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. The success of ongoing efforts to use short-read sequencing to characterize archaeal and bacterial communities requires that researchers strive to expand the depth and breadth of this census.

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“…Other works have developed innovative approaches to reduce the workload of these methods that include a prior analysis of the optimal media to be used 5,13 . If we have test herein different formulas and supplementations, we kept agar as solidifying agent, There are however evidences that gellan gum represents an alternative to agar [19][20][21][22][23] . It is indeed less expensive, is not susceptible to agarases.…”

Section: Discussionmentioning

confidence: 99%

Optimization and standardization of the culturomics technique for human microbiome exploration

Diakite

Dubourg

Dione

et al. 2020

Sci Rep

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Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity.

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Progress in the development of gelling agents for improved culturability of microorganisms

Cited by 52 publications

References 86 publications

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

Status of the Archaeal and Bacterial Census: an Update

Optimization and standardization of the culturomics technique for human microbiome exploration

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