LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria
© Zhou et al; licensee BioMed Central Ltd. 2010
Received: 5 August 2010
Accepted: 23 November 2010
Published: 23 November 2010
In Lactic Acid Bacteria (LAB), the extracellular and surface-associated proteins can be involved in processes such as cell wall metabolism, degradation and uptake of nutrients, communication and binding to substrates or hosts. A genome-scale comparative study of these proteins (secretomes) can provide vast information towards the understanding of the molecular evolution, diversity, function and adaptation of LAB to their specific environmental niches.
We have performed an extensive prediction and comparison of the secretomes from 26 sequenced LAB genomes. A new approach to detect homolog clusters of secretome proteins (LaCOGs) was designed by integrating protein subcellular location prediction and homology clustering methods. The initial clusters were further adjusted semi-manually based on multiple sequence alignments, domain compositions, pseudogene analysis and biological function of the proteins. Ubiquitous protein families were identified, as well as species-specific, strain-specific, and niche-specific LaCOGs. Comparative analysis of protein subfamilies has shown that the distribution and functional specificity of LaCOGs could be used to explain many niche-specific phenotypes.
A comprehensive and user-friendly database LAB-Secretome was constructed to store, visualize and update the extracellular proteins and LaCOGs http://www.cmbi.ru.nl/lab_secretome/. This database will be updated regularly when new bacterial genomes become available.
The LAB-Secretome database could be used to understand the evolution and adaptation of lactic acid bacteria to their environmental niches, to improve protein functional annotation and to serve as basis for targeted experimental studies.
Lactic Acid Bacteria (LAB) have been used for centuries in industrial and artisanal food and feed fermentations as starter cultures and are important bacteria linked to the human gastro-intestinal (GI) tract [1–8]. Phylogenetically they form a relatively compact group of mainly Gram-positive, anaerobic, non-sporulating, low G+C content acid-tolerant bacteria [9–12]. The genera that comprise the LAB belong to the order Lactobacillales, and are primarily Lactobacillus, Pediococcus, Lactococcus, Streptococcus and Leuconostoc, while some peripheral genera are Enterococcus, Oenococcus, Aerococcus, and Carnobacterium. Interestingly, even within such a compact group, vastly divergent phenotypes have been reported, providing indications of high flexibility and adaptation of these species to their living environments [13–16].
Extracellular and surface-associated proteins play a most important role in many essential interactions and adaptations of LAB to their environment [17–26]. By definition these proteins are either exposed on (anchored to membrane GO:0046658, intrinsic to external side of plasma membrane GO:0031233 and the cell wall, GO: 0005618) or released (extracellular milieu, GO:0005576) from the bacterial cell surface. On a genome scale these proteins form a subset of the proteome which contains both the exoproteome  and part of the surface proteome , but excluding the integral membrane proteins (GO: 0005887) and the proteins that are intrinsic to internal side of plasma membrane (GO:0031235). This subset of the proteome belongs to what Desvaux et.al have defined as "secretome"  and is known to mainly be involved processes such as: (1) recognition, binding, degradation and uptake of extracellular complex nutrients, (2) signal transduction, (3) communication with the environment and (4) attachment of the bacterial cell to specific sites or surfaces, e.g. to intestinal mucosa cells of the host [29–37]. Hence, genome-scale comparative analysis of these secretome (surface-associated and released from the cell) proteins may provide an understanding of the molecular function, evolution, and diversity of different LAB species and their adaptation to different environments.
The predicted LAB secretomes (genomes included in the original LaCOG analysis 43 are marked by *).
Secretome proteins (%)
LAB species and strains
The complete results of this study are stored in our open-source database LAB-Secretome http://www.cmbi.ru.nl/lab_secretome with a user-friendly web-interface. An automatic update scheme was constructed to be able to add information to the database on new bacterial genomes.
Results and Discussion
Construction of the secretome protein clusters (LaCOGs)
In this study we focus on those proteins that are predicted to be wholly or largely on the outside of the cell, regardless of the translocation systems. These proteins form a sub-proteome of what Desvaux et.al defined as the "secretome"  by excluding the translocation systems, the integral membrane proteins, and non-protein products. Although we adapt this term "secretome" to describe our protein subset of interest, we must specify that in our analysis the term "secretome" refers to only the proteins that are released from the cells to the extracellular milieu (also called exoproteome), and the proteins that remain cell-surface associated, but nothing else.
Overview of the LaCOGs (genomes included in the original LaCOG analysis 43 are marked by *).
LAB species and strains
Proteins in LaCOG
L.brevis ATCC 367
L.casei ATCC 334 *
L.delbrueckii bulgaricus ATCC BAA-365 *
L.delbrueckii bulgaricus ATCC11842
L.fermentum IFO 3956
L.gasseri ATCC 33323 *
L.helveticus DPC 4571
L.johnsonii NCC 533 *
L.lactis cremoris MG1363
L.lactis cremoris SK11 *
L.lactis lactis IL1403 *
L.mesenteroides ATCC 8293 *
L.plantarum WCFS1 *
L.reuteri F275 JGI
L.reuteri F275 Kitasato
O.oeni PSU-1 *
P.pentosaceus ATCC 25745 *
S.thermophilus CNRZ1066 *
S.thermophilus LMD-9 *
S.thermophilus LMG 18311
False predictions and pseudogenes
The preliminary secretome clusters were curated manually and corrected based on expert knowledge, e.g. for false-positive and false-negative predictions, incorrect gene starts, pseudogenes, etc. Examples of proteins of known intracellular function, but with consistent false-positive extracellular SCL prediction are listed in Additional file 2, sheet S1. In most cases the mis-prediction was caused by an α-helix-like N-terminal sequence in these proteins (possibly as part of the hydrophobic core of a globular protein), leading to the prediction as a signal peptide by LocateP. A further improvement was made by finding and removing those LaCOGs that have proteins which are anchored in the cell membrane with a single N-terminal transmembrane helix, but with the rest of the protein inside the cell (so-called outside-in topology, GO:0031235) [44–53]. By aligning proteins within these LaCOGs we found that these proteins do not have positively charged residues preceding the N-terminal hydrophobic helix, but exclusively have a positively charged residue(s) immediately downstream of the transmembrane helix (examples in Additional file 2, sheet S2). Hence such features could be used for further development of a model for SCL prediction of N-terminally anchored proteins by LocateP.
Nearly 400 pseudogenes were identified, but this is probably an underestimate. In most cases this was due to gene frameshifts, and occasionally to N- or C-terminal truncation of genes. Most of these genes could be concatenated to encode larger proteins with high similarity to known proteins in the LaCOGs. Many of these pseudogenes were initially predicted to encode intracellular proteins by LocateP, but after concatenation these proteins are predicted to be extracellular and/or contain domains of extracellular functionalities. An example are the proteins encoded by adjacent genes LSA1731 and LSA1730 in L.sakei 23K which were annotated as hypothetical proteins. The concatenated protein showed high similarity to proteins in LaCOG02935 which were exclusively cell-surface protein Csc complex family members . In total 129 concatenated pseudoproteins were made with 279 protein fragments (Additional file 3, sheet S1), while 87 pseudogenes could not be combined (Additional file 3, sheet S2).
The LAB-Secretome database
Overview of the extracellular protein families
Only 22 LaCOGs were found to be fully conserved among all 26 LAB secretomes, or only lacking in 1 genome (5 LaCOGs), e.g. the absence of an ATP-dependent protease from LaCOG01453 in P. pentosaceus (Additional file 1, sheet S3).
Most of these LaCOGs contain proteins with universal functionalities involved in cell-wall metabolism, secretion, transport and DNA uptake (Figure 2). Only one conserved family (LaCOG01219) contains proteins of as yet unknown function, but presumably essential as they are conserved in all genomes.
Most common functionalities in the secretomes of LAB
Niche-specific LaCOG families
1/L. acidophilus complex specific
The acidophilus "complex" including the species L. acidophilus, L. johnsonii, L. gasseri, L. delbrueckii ssp bulgaricus and L. helveticus has long been regarded as a phylogenetic subgroup [56–58]. About 30 LaCOGs appear to be specific for these species (Additional file 1, sheet S4). Their proteins include an ABC-type phosphate/phosphonate transport system (LaCOG02118), the aggregation promoting factor (LaCOG90005) [59–61], a putative competence protein (LaCOG03110) and several families of S-layer proteins, which may reflect the special binding function that these S-layer proteins generally share in these acidophilus complex species [62–69]. Interestingly, twenty of these acidophilus complex-specific LaCOGs contain only extracellular proteins of unknown function, and it should be challenging to focus on experimental determination of their function.
If we consider the LAB species L. acidophilus, L. johnsonii, L. gasseri, L. reuteri, and L. salivarius to be specifically found in the GI-tract, then we can identify 17 LaCOGs which are not found outside of this group, of which 13 families contain only proteins of unknown function (Additional file 1, sheet S4). One mucus-binding protein family (LaCOG02280) was found to be specific for these GI-tract LAB, and contains 4 proteins from L. acidophilus, L. gasseri and L. johnsonii. All four proteins are larger than 2300 amino acids, contain a signal peptide with YSIRK domain (Pfam PF04650) and appear to be anchored to the peptidoglycan by an LPxTG cell-wall anchor (Pfam PF00746). Each protein has 5-11 copies of a mucus-binding domain, as defined by Boekhorst et al , showing their particular role in binding to mucus components in the GI-tract [5, 70–72]. The 3 D structure of this domain of 184 residues has recently been determined and shows similarity to the functional repeat found in a family of immunoglobulin-binding proteins .
Twelve LaCOGs appear to be specific for the group of plant-associated species Leuconostoc, Oenococcus, L. plantarum, L. brevis, and P. pentosaceus, of which 7 familes contain only proteins of unknown function (Additional file 1, sheet S4). One of these (LaCOG02876) includes 4 homologous proteins from L.brevis, L.plantarum, O.oeni and L. citreum, which show a high sequence similarity to each other, but the protein from L. plantarum has a much longer serine-rich spacer between the N- and C-terminal domains. A similar domain structure differing in a long serine-rich spacer is seen in the 2 hypothetical proteins from L. plantarum and L. brevis in LaCOG02927.
4/Dairy LAB specific
A few protein families were found only to occur in the secretomes of the dairy LAB S. thermophilus, L. lactis and E. faecalis (Additional file 1, sheet S4). These proteins have functional properties that may be relevant to the dairy niche, e.g. LaCOG00374 contains ABC transporter substrate-binding proteins for polar amino acids, and could possibly be required for growth in milk [74–77]. The L. lactis strains have a single copy of this gene, while the S. thermophilus strains all have 3 consecutive genes encoding paralogs of this amino acid-binding protein. All dairy Streptococcus and Lactococcus strains contain a single gene encoding a beta-lactamase (LaCOG00012) which may play a role in destroying penicillin that these strains may encounter in milk [78–82]. A putative chitinase (glycosyl hydrolase family 18; LaCOG02690) is found exclusively in E. faecalis and in L. lactis strains.
Species-specific and strain-specific LaCOGs
Up to 150 LaCOGs were found to be species-specific or strain-specific (Additional file 1, sheet S5). The distinction is not so clear yet because for some species several strains were sequenced (e.g. L. lactis, S. thermophilus) while for many species only a single strain was sequenced to date. Most of these families are made up solely of hypothetical proteins with highly conserved sequence (Figure 2). L. casei and L. lactis have the highest number of species-specific LaCOGs, indicating that they may have more unique extracellular functions. Examples of species-specific extracellular proteins are the PrgA/PrgB/PrgC surface proteins of E. faecalis[83–85], an alpha-amylase (LaCOG02644) in L. lactis strains, a phospholipase A2 family enzyme (LaCOG99223) in L. casei strains, a cyclo-nucleotide phosphodiesterase (LacOG00213) in S. thermophilus strains, and a mucus-binding protein (LaCOG90010) in L. delbrueckii strains.
Extracellular proteins not in LaCOGs: ORFans and proteins with only distant homologs in non-LAB
About 249 putative extracellular proteins could not be classified into LaCOG families, and comprise 69 proteins that have only distant homologs in non-LAB species and 180 ORFans that are species-specific (Additional file 1, sheets S6 and S7). While the ORFans are nearly all hypothetical proteins of unknown function, the distant homologs also contain proteins with a variety of known functions, such as extracellular enzymes (e.g. xylanase, pectate lyase, endo-beta-N-acetylglucosaminidase, proteases and beta-fructosidase), substrate-binding proteins of transporters, miscellaneous binding proteins and specific bacteriocins. The uniqueness of these proteins suggests that most species or strains have a few unique extracellular proteins that are not found in other sequenced LAB, and may encode unique functions that are related to their environmental niche. Quite a few of the proteins of unknown function are predicted to be lipid-anchored and therefore may represent substrate-binding proteins of uncharacterized transporters.
Specific enzyme families
Examples of specific enzyme and binding-protein sub-families
Specific enzyme families
Subtilisin-like serine protease
L. casei, L. delbrueckii bulgaricus,
L. johnsonii, L. lactis, S. thermophilus
PA domain (PF02225) inserted in the subtilase family domain
L. acidophilus, L. casei
no PA insert domain
mainly in L.plantarum,
different domains for PG binding
aggregation promoting factor related surface protein
not in L.acidophilus group
PG bound by LysM domain; highly conserved C-terminal domain ending in GWY
aggregation promoting factor related surface protein
only in L.delbrueckii bulgaricus,
L.plantarum, L.acidophilus group
highly conserved C-terminal domain ending in WY
aggregation promoting factor related surface protein
only in L.acidophilus group
highly conserved C-terminal domain ending in GWY
glycosyl hydrolase family 70
only in Leuconostoc, L. reuteri,
alpha/beta hydrolase of unknown function (DUF915)
alpha/beta hydrolase (DUF915)
alpha/beta hydrolase (DUF915)
only in L. delbrueckii bulgaricus, L.plantarum , L.casei
alpha/beta hydrolase (DUF915)
only in L.plantarum , L.casei , L.sakei
not in L.acidophilus group
with GDSL-like motif
general cell surface hydrolase
cell surface hydrolase membrane-bound (putative)
only in L.delbrueckii bulgaricus, L.plantarum,L.casei , L.fermentum
only in L.plantarum , L.delbrueckii bulgaricus, P.pentosaceus
MUB domain, Gram positive anchor
only in L.plantarum, L.delbrueckii bulgaricus, P.pentosaceus, L.acidophilus group
Collagen binding domain, Gram positive anchor
not in L.acidophilus group
MucBP domain (Classical), Gram positive anchor
not in L.acidophilus group
Leucine Rich Repeat, PT repeat
MUB domain, Gram positive anchor
many pseudogenes, most L.acidophilus group proteins have YSIRK-type signal peptide
MUB domain, Gram positive anchor
only in L.acidophilus group
very large, YSIRK-type signal peptide
MUB domain, Gram positive anchor
5 of 10 are pseudogenes; YSIRK SP in L.acidophilus group members
MUB domain, Gram positive anchor
only in L.acidophilus group
all pseudogenes; YSIRK type signal peptide
Chitin binding domain
E.faecalis, L.plantarum, L.sakei, L.lactis
maybe related to niche
von Willebrand factor type A domain, Cna protein B-type domain
only in L.lactis, E.faecalis, L.citreum, L.casei
Specific binding-protein families
Many extracellular proteins contain known domains for binding to macromolecular substrates. In addition to domains for binding to the cell wall of the producing cell (e.g. LysM, SH3), several other domains are found which are related to binding to host macromolecules (e.g. domains annotated as mucus-binding, chitin-binding, collagen-binding, fibronectin-binding, carbohydrate-binding, etc) (Table 3). Some of these annotations derive from in vitro binding studies and may not reflect in vivo functions. In LAB, mucus-binding domains (MUB, MucBP) are found in many proteins and are thought to play a role in binding to the host GI-tract mucus layer [57, 93, 94]. An enormous variety is found in the size of these mucus-binding proteins and in the number of mucus-binding domains. We have made a preliminary separation into 7 different subfamilies of mucus-binding proteins based on protein size, sequence homology, domain composition and phylogeny (Table 3). The three largest subfamilies are (1) LaCOG00885 containing 11 members from different LAB but not from L. acidophilus group members, (2) LaCOG01470 with 28 members, found in many LAB, and (3) LaCOG03211 which includes 10 proteins. The proteins of LaCOG00885 contain solely the MucBP domains as defined by Pfam (PF00746), while the proteins of the other two LaCOGs possess multiple copies of the larger MUB domains as defined by Boekhorst et al. (see also Figure 2 in). Many mucus-binding proteins of L. acidophilus group members contain an N-terminal [Y/F]SIRKxxxGxxS-containing signal peptide (PF04650) which was earlier reported as a typical characteristic of the L. acidophilus MUB proteins [94, 96], and may relate to a specific function in sorting or folding [97, 98]. Furthermore, it is striking that many large genes encoding mucus-binding proteins are pseudogenes (e.g. in LaCOG01470, LaCOG03211 and LaCOG99309). While it is unlikely that these are all due to sequencing errors, it is not clear yet whether these are truly pseudogenes, or possibly may encode functional proteins after transcription with strand-slipping [5, 71].
Lactic Acid Bacteria (LAB) occur naturally in many different fermentation environments such as plant, meat, dairy and cereal. Overall similarities have been identified among the genomes of many LAB species [61, 99–105]. However, bio-diversity has also been reported frequently, showing that subtle variations in presence or absence of proteins and functional domain composition might lead to important traits during bacterial adaptation to their living environments [106–113]. Our comparative research on extracellular and surface-associated protein families has provided a more solid basis for this hypothesis. Universal families have been identified which are apparently essential for survival of all LAB, but also species-specific protein families. Besides the clustered proteins with known functions, many families of hypothetical proteins and unique proteins (ORFans and proteins with only distant homologs in non-LAB) were found.
Protein clustering supports niche-dependent features of specific subgroups of LAB (e.g. the L. acidophilus group) and could aid in linking bacterial phenotypes to genotypes. The distinct sub-families of the different LaCOGs have provided clues for adaptation of the bacterial cells to their living environment, such as the GI-tract. The result of this study can be used as leads for experimental work on the molecular evolution, diversity, function and adaptation of bacteria to specific environments.
Our clustering methods and database structure were designed in a way that allows adoption to other groups of bacteria than LAB. The analysis results are stored in a queryable database which provides vivid browsing functions for users, and will be updated regularly to guarantee the continuation of the service to the biology community. Our clustering information into families could definitely help in checking the quality of newly sequenced genomes and for genome (re-)annotation.
Genome sequences and bioinformatics tools used in this research
The genome sequences of 26 selected representative lactic acid bacteria, including the protein functional annotation and the gene contexts, were obtained from the NCBI bacterial genome database (version 15 Aug., 2008) .
BlastP (default cutoff values of E < 1, low-complexity filter disabled)  and Inparanoid  were used for sequence homology and orthology searches, respectively. Protein subcellular location (SCL) was predicted by LocateP . Multiple sequence alignments were constructed using Muscle . Motif searches were performed using MEME and MAST . Protein domains (version Dec. 2008)  originating from the Pfam database [119–121] and additional HMMs reported in other studies [54, 71, 96, 122–124] were searched using HMMER  with the respective cut-off of each model. The domain functions were obtained from the GO database  using the PFAM2GO dataset .
The LAB-Secretome database was created in MySQL and the database interface was written in PHP (version5.2.7). Visualization of the protein domain composition was made using scalable vector graphics (SVG).
Protein clustering into orthology groups (LaCOGs)
First, the 22,191 proteins in 3195 LaCOGs generated by Makarova et.al from 12 LAB genomes were used as the basis for protein clustering. All protein sequences from 14 newly sequenced LAB genomes were searched against the Makarova LaCOG set using BlastP. The proteins that have high homology to the existing LaCOGs were then selected using a revised criterion based on the well-known COG extension rule "uniform top 3": if all the top 3 (in case of LaCOG size of 2, the top 2 hits were taken) BlastP hits of a query protein belong to the same LaCOG (LaCOG size bigger than or equals to 2), then the query protein is added to this LaCOG.
Since the above-mentioned extension was purely based on the homologs of proteins that were already included in the LaCOGs by Makarova et al., the specific proteins from newly sequenced species, e.g. L. reuteri, were not added due to the absence of the "seeding sequences" for BlastP. In order to cluster all proteins that originated from the newly sequenced genomes, a complete all-to-all Inparanoid  search was performed in a parallel fashion with the proteins encoded in the 14 new genomes to identify orthologous proteins. Cut-off settings of bit score 50 and sequence overlap of 50% were used. The proteins with all-to-all bidirectional-best-hit (BBH) relationship [128, 129] were clustered into groups, meaning that in any such group, each member is the BBH of another member. This stringent criterion generates new cores of orthologous proteins.
Using the core ortholog clusters and the extended LaCOGs made in step one, the proteins that were not previously included in any clusters, including those proteins from Makarova LaCOGs containing only 1 member, were Blasted as queries. In this step, the revised criterion "uniform top 3" was used and new LaCOGs were made.
The newly made LaCOGs were merged with the extended Makarova LaCOGs, and the newly made ones were assigned coding numbers starting with "9" in their names, e.g. LaCOG90001, to distinguish them from the extended Makarova LaCOGs.
LaCOG quality control
In order to check the quality of the merged LaCOGs, an iterative BlastP search was performed using the clustered proteins as queries against all the proteins that were not included in any constructed LaCOGs, using the criteria of 1E-3 and query-hit protein length ratio of 0.6, which has been tested by Boekhorst et. al. for distant homolog identification. This iterative search found that only 13 non-clustered proteins (mostly hypothetical proteins) had a distant homolog in 11 different LaCOGs, indicating that our clustering methods have extensively included most of the proteins into possible homologous clusters.
ORFans and proteins with only non-LAB distant homologs
The LAB proteins that could not be clustered into LaCOGs by the previously described procedures were then collected and Blasted against all completely sequences non-LAB bacterial genomes (both Gram- and Gram+ species). The same criterion of distant homolog identification  was utilized. Proteins that had no homologs in any other species were named "ORFans".
Secretome LaCOG extraction
The clustering information of merged LaCOGs, proteins that have only distant homologs in non-LAB species and the ORFans was then combined with the SCL prediction made by LocateP (Table 1). Initially, only the LaCOGs that had at least half of the members with a predicted secretome SCL corresponding to (1) lipid-anchored; (2) N-/C-terminally anchored; (3) secreted by Tat- or Sec- pathway; (4) secreted via non-classical pathways, or (5) cell-wall anchored were identified as the secretome LaCOGs. Later, all other LaCOGs were manually inspected, and a few families were identified with a mixture of secretome and intracellular proteins; only the secretome proteins were added to the database. The same classification was applied to the secretome ORFans and proteins that have only distant homologs in non-LAB species. The resulting clusters of secretome proteins, the "secretome", can be further extended by similar processes when new (LAB) genome sequences become available.
Proteins that are exported by unknown mechanisms and so-called "moon-lighting" proteins (known intracellular function, but often also found on the outside of the cell)  were not considered as their extracellular SCL cannot be predicted.
In order to obtain as accurate as possible prediction of secretome proteins and their classification into LaCOGs, we performed a throughout manual inspection on all the secretome proteins, including the ORFans and the ones included in LaCOGs. All proteins were double checked for the ORF-calling quality by the criteria combining protein length, possible alternative start (end) codon, multiple sequence alignments, protein domain composition and SCL prediction consistency.
Incorrectly chosen start codons in the original annotations were corrected based on sequence alignment with protein family members, position of putative ribosome-binding sites, and known features of signal peptides. Pseudogenes were initially identified when BLASTP analysis of the encoded proteins showed that they belong to extracellular protein families in LaCOGs, but that they represented only a fragment of the protein. By analysis of the coding region of these pseudogenes with their adjacent nucleotide sequences we could generally identify frameshifts, such that the missing protein part(s) were found to be encoded in a different reading frame. In these cases, the entire opening-reading frames were translated into protein fragments, regardless of the absence of start codons, and these protein fragments were concatenated to form new protein sequences that share high similarity to other known full-length proteins. In a few cases, ORFans were also identified as pseudogenes when they lacked a signal peptide, but otherwise contained protein domains typical of extracellular proteins.
Generally, we expected the ORFans to be real genes that represent unique functionality to the specific LAB in which they occur. However, because the average size of these hypothetical ORFs was below 100 amino acids, it is possible that some small ORFans could as well be wrongly predicted ORFs or pseudogenes. Proteins smaller than 80 amino acids containing only a Sec-type N-terminal signal sequence were removed from the set of predicted extracellular proteins, since their C-terminal part is generally too small to represent an extracellular domain. Moreover, many of such small proteins with a single predicted TM helix are now increasingly considered as small integral membrane proteins .
M Zhou was funded by the BioRange programme of the Netherlands Bioinformatics Centre (NBIC) which is supported by a BSIK grant through the Netherlands Genomics Initiative (NGI). DT, MW and RS are partly supported by the TI Food and Nutrition and the Kluyver Centre for Genomics of Industrial Fermentation.
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