Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case

Young, J. C.; Pan, Chongle; Adams, Rachel M; Brooks, Brandon; Banfield, Jillian F.; Morowitz, Michael J.; Hettich, Robert L.

doi:10.1002/pmic.201400563

Cited by 57 publications

(79 citation statements)

References 67 publications

(107 reference statements)

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“…Whole community shotgun genomics or proteomics with in silico analysis of potential community interactions could offer a powerful alternative. 44,45 In addition, studying lipase production and the influence of GML in the context of the dynamics of the in vivo bacterial community is a natural extension of these investigations.…”

Section: Discussionmentioning

confidence: 99%

Glycerol Monolaurate Inhibits Lipase Production by Clinical Ocular Isolates Without Affecting Bacterial Cell Viability

Flanagan

Khandekar

Zhu

et al. 2016

Invest. Ophthalmol. Vis. Sci.

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PURPOSE. We sought to determine the relative lipase production of a range of ocular bacterial isolates and to assess the efficacy of glycerol monolaurate (GML) in inhibiting this lipase production in high lipase-producing bacteria without affecting bacterial cell growth.METHODS. Staphylococcus aureus, Staphylococcus epidermidis, Propionibacterium acnes, and Corynebacterium spp. were inoculated at a density of 10 6 /mL in varying concentrations of GML up to 25 lg/mL for 24 hours at 378C with constant shaking. Bacterial suspensions were centrifuged, bacterial cell density was determined, and production of bacterial lipase was quantified using a commercial lipase assay kit.RESULTS. Staphylococcus spp. produced high levels of lipase activity compared with P. acnes and Corynebacterium spp. GML inhibited lipase production by Staphylococcal spp. in a dosedependent manner, with S. epidermidis lipase production consistently more sensitive to GML than S. aureus. Glycerol monolaurate showed significant (P < 0.05) lipase inhibition above concentrations of 15 lg/mL in S. aureus and was not cytotoxic up to 25 lg/mL. For S. epidermidis, GML showed significant (P < 0.05) lipase inhibition above 7.5 lg/mL. CONCLUSIONS.Lipase activity varied between species and between strains. Staphylococcal spp. produced higher lipase activity compared with P. acnes and Corynebacterium spp. Glycerol monolaurate inhibited lipase production by S. aureus and S. epidermidis at concentrations that did not adversely affect bacterial cell growth. GML can be used to inhibit ocular bacterial lipase production without proving detrimental to commensal bacteria viability.

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Section: Discussionmentioning

confidence: 99%

Glycerol Monolaurate Inhibits Lipase Production by Clinical Ocular Isolates Without Affecting Bacterial Cell Viability

Flanagan

Khandekar

Zhu

et al. 2016

Invest. Ophthalmol. Vis. Sci.

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“…Changes in the characteristics of the microbiome over time might also be indicative of changes in the quality of the social or broader environment (Amato et al., ; Tung et al., ) and can be significantly differentiated among individuals within a population (Klein‐Jöbstl et al., ). Additionally, studies in model organisms have used proteomic analysis of faecal samples to noninvasively monitor host–microbe interaction during development (e.g., Young et al., ) and disease processes (e.g., Yau, Leong, Zeng, & Wasinger, ).…”

Section: Past and Future Opportunitiesmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2018

Evolutionary Applications

146

108

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The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD‐seq) require large amounts of high‐quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low‐quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next‐generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

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“…Changes in the characteristics of the microbiome over time might also be indicative of changes in the quality of the social or broader environment (Amato et al, 2013;Tung et al, 2015), and can be significantly differentiated amongst individuals within a population (Klein-Jöbstl et al 2015). Additionally, studies in model organisms have used proteomic analysis of faecal samples to noninvasively monitor host-microbe interaction during development (e.g., Young et al, 2015) and disease processes (e.g., Yau et al, 2013).…”

Section: Health and Dietmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2017

Preprint

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Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically-driven declines, which are unlikely to abate without intensive management efforts that often include MIS approaches. Here we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy datasets and recommend how to address the challenges of moving between traditional and next generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3209v1 | CC BY 4.0 Open Access |

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Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case

Cited by 57 publications

References 67 publications

Glycerol Monolaurate Inhibits Lipase Production by Clinical Ocular Isolates Without Affecting Bacterial Cell Viability

Glycerol Monolaurate Inhibits Lipase Production by Clinical Ocular Isolates Without Affecting Bacterial Cell Viability

Genetic and genomic monitoring with minimally invasive sampling methods

Genetic and genomic monitoring with minimally invasive sampling methods

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