4 Genome Data Drives Change at Culture Collections

McCluskey, Kevin; Wiest, Aric; Boundy‐Mills, Kyria

doi:10.1007/978-3-642-45218-5_4

Cited by 8 publications

(4 citation statements)

References 44 publications

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“…In the current era of powerful DNA sequencing and genetic manipulation tools, study and use of microbial species beyond the small set of commonly used laboratory or model strains is becoming more feasible. Industrial microbiologists are now tapping culture collections and nature to select parent strains that already have a number of promising characteristics [4,5,29]. These yeasts can either be developed as industrial organisms, or their properties can be engineered into model or industrial organisms such as Saccharomyces cerevisiae or Escherichia coli [40].…”

Section: Discussionmentioning

confidence: 99%

Carbon source utilization and inhibitor tolerance of 45 oleaginous yeast species

Sitepu

Selby

Lin

et al. 2014

Journal of Industrial Microbiology and Biotechnology

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121

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Conversion of lignocellulosic hydrolysates to lipids using oleaginous (high lipid) yeasts requires alignment of the hydrolysate composition with the characteristics of the yeast strain, including ability to utilize certain nutrients, ability to grow independently of costly nutrients such as vitamins, and ability to tolerate inhibitors. Some combination of these characteristics may be present in wild strains. In this study, 48 oleaginous yeast strains belonging to 45 species were tested for ability to utilize carbon sources associated with lignocellulosic hydrolysates, tolerate inhibitors, and grow in medium without supplemented vitamins. Some well-studied oleaginous yeast species, as well as some that have not been frequently utilized in research or industrial production, emerged as promising candidates for industrial use due to ability to utilize many carbon sources, including Cryptococcus aureus, Cryptococcus laurentii, Hanaella aff. zeae, Tremella encephala, and Trichosporon coremiiforme. Other species excelled in inhibitor tolerance, including Candida aff. tropicalis, Cyberlindnera jadinii, Metschnikowia pulcherrima Schwanniomyces occidentalis and Wickerhamomyces ciferii. No yeast tested could utilize all carbon sources and tolerate all inhibitors tested. These results indicate that yeast strains should be selected based on characteristics compatible with the composition of the targeted hydrolysate. Other factors to consider include the production of valuable co-products such as carotenoids, availability of genetic tools, biosafety level, and flocculation of the yeast strain. The data generated in this study will aid in aligning yeasts with compatible hydrolysates for conversion of carbohydrates to lipids to be used for biofuels and other oleochemicals.

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Section: Discussionmentioning

confidence: 99%

Carbon source utilization and inhibitor tolerance of 45 oleaginous yeast species

Sitepu

Selby

Lin

et al. 2014

Journal of Industrial Microbiology and Biotechnology

Self Cite

121

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“…Examples of some prominent microbe collections in the United States, their major holdings and URLs are listed in Table 1 ( McCluskey et al 2016). Curators of these collections have interacted in recent years through the US Culture Collection Network (McCluskey et al 2014a;McCluskey et al 2014b;Boundy-Mills et al 2015;McCluskey et al 2016;McClusskey et al 2017b). Because this publication arose from discussions at a USCCN gathering, it focuses on US collections.…”

Section: Diversity Of Microbial Collectionsmentioning

confidence: 99%

Preserving US microbe collections sparks future discoveries

Boundy‐Mills

McCluskey

Elia

et al. 2020

Journal of Applied Microbiology

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Collections of microorganisms are a crucial element of life science research infrastructure but are vulnerable to loss and damage caused by natural or man-made disasters, the untimely death or retirement of personnel, or the loss of research funding. Preservation of biological collections has risen in priority due to a new appreciation for discoveries linked to preserved specimens, emerging hurdles to international collecting and decreased funding for new collecting. While many historic collections have been lost, several have been preserved, some with dramatic rescue stories. Rescued microbes have been used for discoveries in areas of health, biotechnology and basic life science. Suggestions for long-term planning for microbial stocks are listed, as well as inducements for long-term preservation.

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“… 6 Living collections may be established in support of a specific research area 1 , 2 or as a diverse taxonomy resource, 7 , 8 and many culture collections have found new value as technology has advanced. 9 , 10 Most living collections allow repurposing of holdings without the need for consent of the depositor, although some new uses may require benefit sharing under the Nagoya Protocol. 11 Changing legal or regulatory circumstances requires collections to address issues of sustainability and the overall trend is toward increased impact through implementing best practices for quality management, data sharing, and visibility of validated and authenticated materials.…”

Section: Introductionmentioning

confidence: 99%

A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines

McCluskey

2017

Biopreservation and Biobanking

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Formal living collections have unique characteristics that distinguish them from other types of biorepositories. Comprising diverse resources, microbe culture collections, crop and biodiversity plant germplasm collections, and animal germplasm repositories are commonly allied with specific research communities or stakeholder groups. Among living collections, microbial culture collections have very long and unique life histories, with some being older than 100 years. Regulatory, financial, and technical developments have impacted living collections in many ways. International treaty obligations and restrictions on release of genetically modified organisms complicate the activities of living collections. Funding for living collections is a continuing challenge and threatens to create a two-tier system where medically relevant collections are well funded and all other collections are underfunded and hence understaffed. Molecular, genetic, and whole genome sequence analysis of contents of microbes and other living resource collections bring additional value to living collections.

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4 Genome Data Drives Change at Culture Collections

Cited by 8 publications

References 44 publications

Carbon source utilization and inhibitor tolerance of 45 oleaginous yeast species

Carbon source utilization and inhibitor tolerance of 45 oleaginous yeast species

Preserving US microbe collections sparks future discoveries

A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines

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