Metaproteomics Approach To Study the Functionality of the Microbiota in the Human Infant Gastrointestinal Tract

Klaassens, Eline S.; Vos, Willem M. de; Vaughan, Elaine E.

doi:10.1128/aem.01921-06

Cited by 157 publications

(120 citation statements)

References 26 publications

Supporting

Mentioning

112

Contrasting

Unclassified

Order By: Relevance

“…To our knowledge, this is the first report on the adaptive response of the gut metaproteome to dietary challenge. Since the first gel-based metaproteome published in 2007 (Klaassens et al, 2007) and the state-of-the art LC-MS/MS work by Verberkmoes et al (2009), the size of genomic databases has been rising exponentially. Nevertheless, annotation of peptide spectra remains challenging and functional interpretation based on the occurrence of dominant proteins is limited, that is, taking into account the high degree of diversity of the intestinal microbial ecosystem, we still profit only from a narrow window of analysis at the proteome level (Rooijers et al, 2011;Haange et al, 2012;Kolmeder et al, 2012;Perez-Cobas et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

High-fat diet alters gut microbiota physiology in mice

Daniel¹,

Gholami²,

Berry³

et al. 2013

The ISME Journal

590

386

View full text Add to dashboard Cite

The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by highcalorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared-(FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via highresolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.

show abstract

Section: Discussionmentioning

confidence: 99%

High-fat diet alters gut microbiota physiology in mice

Daniel¹,

Gholami²,

Berry³

et al. 2013

The ISME Journal

590

386

View full text Add to dashboard Cite

show abstract

“…The physicochemical composition and especially the high protein or fat content may interfere with experimental procedures for RNA and protein isolation that work well with laboratory media. A number of studies have appeared that describe successful transcriptome or proteome analyses on samples from fermented substrates and even from highly complex materials such as fecal samples (81,178). Most studies of dairy fermentations use skim milk, in which the precipitation of casein may be prevented by pretreatment with sodium citrate (126,139).…”

Section: Genomics Approaches For Mixed-culture Researchmentioning

confidence: 99%

Unraveling Microbial Interactions in Food Fermentations: from Classical to Genomics Approaches

Sieuwerts

Bok

Hugenholtz

et al. 2008

Appl Environ Microbiol

270

178

View full text Add to dashboard Cite

3Fermentation, the microbial degradation of organic compounds without net oxidation, is an important process in the global carbon cycle and is also exploited worldwide for the production and preservation of food. It is one of the oldest food-processing technologies known, with some records dating back to 6,000 B.C. (50). The link between food and microbiology was laid by Pasteur, who found that yeasts were responsible for alcoholic fermentation (106). Since that discovery, scientific and industrial interests in food microbiology started to grow and continue to increase today. The number of food products that rely on fermentation in one or more steps of their production is tremendous. They form an important constituent of the daily diet and rank among the most innovative product categories in the food industry.Most of the important microorganisms applied in the production of fermented foods have been studied for decades, yielding a wealth of information on their physiology and genetics in relation to product functionalities, such as the development of flavor, taste, and texture. The recent emergence of genomics has opened new avenues for the systematic analysis of microbial metabolism and the responses of microorganisms to their environment. Additionally, genomics has boosted research on important food microbes (22,90,93). Much of this research focuses on the performance of a single strain, including its interactions with the food matrix. However, food fermentations are typically carried out by mixed cultures consisting of multiple strains or species. Population dynamics play a crucial role in the performance of mixed-culture fermentations, and for many years, studies on mixed-culture food fermentations have focused on analyzing population dynamics using classical and molecular methods. Many of these studies are mainly descriptive, and relatively little is known about the mechanisms governing population dynamics in general and the molecular interactions that occur between the consortium members in particular. The availability of genome sequences for several species that are of industrial importance as well as technological advances in functional genomics enable new approaches to study food microbiology beyond the single species level and allow an integral analysis of the interactions and metabolic activity in mixed cultures.Here we review the current knowledge on important food fermentation processes, focusing on the bacterial interactions.In addition, we illustrate how genomics approaches may contribute to the elucidation of the interaction networks between microbes, including interactions with the food environment. This information may find application in the industry through rational optimization and increased control over mixed-culture fermentations.

show abstract

“…These limitations can be overcome by directly assessing proteins, because the genes must have been transcribed and translated to produce a protein product. However, to date only a couple of microbial proteins have been identified from the human gut and these were obtained by twodimensional (2D) PAGE (Klaassens et al, 2007), followed by excision and de novo sequencing of targeted spots on the gel.…”

Section: Introductionmentioning

confidence: 99%

Shotgun metaproteomics of the human distal gut microbiota

et al. 2008

View full text Add to dashboard Cite

The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

show abstract

Metaproteomics Approach To Study the Functionality of the Microbiota in the Human Infant Gastrointestinal Tract

Cited by 157 publications

References 26 publications

High-fat diet alters gut microbiota physiology in mice

High-fat diet alters gut microbiota physiology in mice

Unraveling Microbial Interactions in Food Fermentations: from Classical to Genomics Approaches

Shotgun metaproteomics of the human distal gut microbiota

Contact Info

Product

Resources

About