REVIEW

published: 28 January 2020

doi: 10.3389/fmicb.2019.03084

The Progress of Multi-Omics

Technologies: Determining Function
in Lactic Acid Bacteria Using a
Systems Level Approach
Shane Thomas O’Donnell 1,2,3 , R. Paul Ross 1,2,3 and Catherine Stanton 1,3*
1
Teagasc Food Research Centre, Moorepark, Fermoy, Ireland, 2 Department of Microbiology, University College Cork –
National University of Ireland, Cork, Ireland, 3 APC Microbiome Ireland, Cork, Ireland

Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact
ranging from commercial to health domains. A vast amount of research has been carried
out on these microbes, deciphering many of the pathways and components responsible
for these desirable effects. However, a large proportion of this functional information
has been derived from a reductionist approach working with pure culture strains. This
provides limited insight into understanding the impact of LAB within intricate systems
such as the gut microbiome or multi strain starter cultures. Whole genome sequencing
Edited by: of strains and shotgun metagenomics of entire systems are powerful techniques that
Konstantinos Papadimitriou,
Agricultural University of Athens, are currently widely used to decipher function in microbes, but they also have their
Greece limitations. An available genome or metagenome can provide an image of what a strain
Reviewed by: or microbiome, respectively, is potentially capable of and the functions that they may
Jasna Novak,
University of Zagreb, Croatia
carry out. A top-down, multi-omics approach has the power to resolve the functional
Fabio Minervini, potential of an ecosystem into an image of what is being expressed, translated and
University of Bari Aldo Moro, Italy produced. With this image, it is possible to see the real functions that members of a
*Correspondence: system are performing and allow more accurate and impactful predictions of the effects
Catherine Stanton
[Link]@[Link] of these microorganisms. This review will discuss how technological advances have the
potential to increase the yield of information from genomics, transcriptomics, proteomics
Specialty section:
and metabolomics. The potential for integrated omics to resolve the role of LAB in
This article was submitted to
Systems Microbiology, complex systems will also be assessed. Finally, the current software approaches for
a section of the journal managing these omics data sets will be discussed.
Frontiers in Microbiology
Keywords: lactic acid bacteria, multi-omics, microbiome, genomics, transcriptomics, proteomics, metabolomics,
Received: 08 July 2019
meta-omics
Accepted: 20 December 2019
Published: 28 January 2020
Citation: INTRODUCTION
O’Donnell ST, Ross RP and
Stanton C (2020) The Progress
Sequencing the first whole genome of a bacterial strain, namely Haemophilus influenzae, in 1995
of Multi-Omics Technologies:
Determining Function in Lactic Acid
was a milestone in molecular biology for a number of reasons (Fleischmann et al., 1995), one of
Bacteria Using a Systems Level which was heralding in an era rich in information where the volume of data produced was beyond
Approach. Front. Microbiol. 10:3084. being completely interpreted. Subsequent genomic data sets derived from bacteria elucidated gene
doi: 10.3389/fmicb.2019.03084 functions, metabolic networks, biological pathways, microbial evolution and genome structure

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O’Donnell et al. Multi-Omics Technologies for LAB

significantly enhancing our understanding of bacterial function scope of the lab bench. An appreciation of the strengths and
and potential (Kanehisa and Goto, 2000; Ley et al., 2006). limitations of many of these technologies will allow researchers
However, the challenge in deciphering relevant genetic to answer more complex questions and generate more general
information from the background genetic material was almost an conclusions. This is a constant arms race as the technologies
impossible task. To combat this, more information was required. that underpin the generation of these omic and meta’omic
Information on the transcription of the genetic material and data sets are constantly advancing. The scope of analysis
subsequent production of proteins was necessary. The targets ranges from entire community samples of 1012 microbes to
of these proteins and the molecules they interact with had to be exploring the components of single cells. Higher throughput
determined. Nuanced epigenetic triggers and the metabolites machines are facilitating deeper sequencing than ever before.
that are ultimately produced are all crucial to understanding the This sequencing depth is opening new potential use cases
system as a whole. Indeed, much of the observed phenotype in such as metatranscriptomics of the gut microbiome. Integrating
a system can be explained in the context of these data sets when these large data sets to provide a systems level view will
interpreted correctly. reveal previously unattainable information on the individual
Biological systems rely on the DNA – RNA – protein microbes involved.
information transfer paradigm that determines the phenotype LAB are uniquely placed to take full advantage of these
of an organism. Biologists have analyzed these “omes” for a fundamental changes in approach. Notably, LAB have been the
number of years in the form of genomics, transcriptomics and subject of extensive research exploring specific attributes and
proteomics. In addition to these, epigenomics and metabolomics functions of isolated cultures (Noike et al., 2002; Leroy and De
have recently been used to answer specific questions relating Vuyst, 2004). In depth analysis of individual LAB strains has
to the many functions of an organism. Given the year on year provided a wealth of information on their biological processes
advances in “omics” technologies, the volume of information and functionality in a variety of publically available databases.
that can be gathered in individual studies is expanding rapidly. Multi-omics technologies stand ready to exploit this information
Furthermore, the current high throughput nature of these on LAB to decipher and predict many functions of interest using
techniques has increased accessibility to this information in terms a systems level approach. Inter-microbe interactions, particularly
of time and cost. This has placed many researchers in a situation within starter cultures, are some of the first to witness the
where they can collect several omics data sets on the same potential in these advances (Sattin et al., 2016; Sirén et al., 2019).
experimental samples. In order to draw more comprehensive Similarly, multi-omics technologies are currently being used to
conclusions on biological processes these data sets must be tackle more complex systems such as the gut microbiome and
integrated and analyzed as a holistic system. host-microbe interactions (Turroni et al., 2016; Huang et al.,
Technologies involved in a multi-omics approach share 2017; Wang et al., 2019). This emerging field is capable of
several commonalities, some of which contrast with the providing a platform for more accurate functional prediction of
original approach of molecular biologists. For the most part, LAB in a variety of complex environments.
molecular biology has utilized a reductionist approach to date. In this review, we will discuss the current most popular
This methodology involves breaking a complex problem into combinations of different omics technologies to facilitate
its constituent parts and solving them individually. While accurate functional prediction for LAB. The most recent advances
reductionism has had significant successes, particularly when in the relevant technologies will be mentioned, while the potential
the experimental subject is controlled by a single component they hold for deciphering the final phenotype of these microbes
(Isberg and Falkow, 1985), or can be explained by interactions will be assessed. Finally, the computational barriers associated
between single molecules (Krebs, 1940), it also has substantial with integrating complex and diverse data sets will be discussed.
limitations. These limitations are caused by the process of
isolating components of a complex system; often the nature
of their role in the system is lost. This is the most significant THE POTENTIAL FOR FUNCTIONAL
advantage that omics technologies can have compared to a PREDICTION IN LAB USING OMICS
reductionist approach. Maintaining these components in the TECHNOLOGIES
system allows observation in a realistic environment where
emergent properties can also be studied. These high throughput, LAB are among the most industrially significant groups of
top down methods also provide a phenomenal volume of data in bacteria. These versatile microbes have a variety of potential
comparison to the reductionist approach. For example, as much functions that are applied in many sectors. Food production,
as six terabytes of information can be generated by processing health promotion, production of antimicrobials and in vivo
samples in tandem on an Illumina NovaSeq 6000. Finally, omics fermentation all see benefit from this group of microorganisms.
technologies require significant computational infrastructure in These diverse functions encoded within single genomes are a
the form of novel algorithms and software to process and analyze source of valuable information available for exploitation. As
the information produced (Berger et al., 2013). a result, these processes have been studied extensively using
This has placed researchers in a situation where they must in vitro, in vivo and more recently in silico techniques to
adapt to maximize the results from biological data. Biologists determine the critical pathways underpinning the phenotypes.
must acquire skills in managing and manipulating these vast Analysis of these molecular pathways has resulted in more
quantities of data to resolve experimental questions outside the accurate use of LAB in commercial endeavors such as starter

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O’Donnell et al. Multi-Omics Technologies for LAB

fermentation cultures and probiotic supplements (Leroy and motifs and patterns in specific alignment of DNA bases e.g.,
De Vuyst, 2004; Muñoz-Atienza et al., 2013). Deciphering the Shine-Dalgarno, allows software to detect important genes
underlying biological attributes associated with these critical such as cluster specific transcription factors and the promoters
microbes allows greater understanding of their current roles and associated with said genes (Wolf et al., 2018). Such methods
may reveal new applications. However, this scrutiny has often can be used in conjunction with comparative genomics to
focused on a single element of interest in isolation, instead of predict the production of difficult to detect molecules such
taking the entire system into account. as secondary metabolites in the form of antibiotics, toxins
A more inclusive approach is possible with diverse sets and immunosuppressives (Zerikly and Challis, 2009; Weber
of information interrogated by omics technologies. To date, et al., 2018). Mining genomes for well-known genes is more
many groups have utilized both omics and multi-omics data straightforward using BLAST or DIAMOND (Altschul et al.,
sets to advance this field and progress knowledge of LAB 1990; Buchfink et al., 2014). Searching the DNA or protein
function (Lahtvee et al., 2011; Rebollar et al., 2016; Huang sequence of the element of interest against your genome will
et al., 2017; Filannino et al., 2018; Ellepola et al., 2019). The provide probability-based results on its presence in the genome.
consistent progression of new technologies and methodologies This information is the bedrock on which the multi-omics
has resulted in many studies providing crucial information on integration is built.
the function of LAB. Progress in this manner also provides Mining genomic information on its own may direct
direction for future work with these microbes. Studies using experimentation or suggest mechanisms for known functional
multi omics for mammalian or bacterial cells may pre-empt attributes. This was exemplified by analysis of genomic data
similar work with LAB. New methodologies incorporating in Lactobacillus ruminis revealing the presence of functional
omics technologies are often applicable to a variety of research flagellar apparatus in the form of 45 flagellar genes (Neville
topics. These studies will be discussed to gain insight into the et al., 2012). Robust flagellar apparatus suggests L. ruminis
potential use cases for LAB. Translating the relevant findings is a motile microbe and presents a mechanism for pro-
in multi omics research will focus on what can be discovered inflammatory tendencies. Despite not expressing flagella in
in LAB within ecosystems they inhabit and their common culture media, strains with the genomic capacity to produce
commercial applications. The influence exerted by the new flagella were observed to partially recover this ability in vivo.
technological advancements will also be assessed for their Gene clusters for crucial mucus binding pili have been detected
direct effect on LAB. in several LAB (Douillard et al., 2013). This gene cluster explains
Basic functions of LAB are well understood, as are the cellular L. rhamnosus’ capacity to adhere to the intestinal mucosa
processes underlying them. With this foundation of knowledge, (Kankainen et al., 2009). In a similar fashion, gene clusters that
research into LAB is in a prime position to exploit the coming are capable of producing a broad range of bacteriocins have been
wave of omics technologies. The sections below document the reported. This information led to observe Lactobacillus salivarius
strengths and limitations of each omics technology, the impact of outcompeting Listeria monocytogenes utilizing these compounds
each omic data set on inferring LAB function to date, the relevant (Corr et al., 2007).
advancement in technology and how these new methodologies Appropriate use of secondary metabolite software tools for
may accelerate future progress. analyzing the genome has resulted in the discovery of many
novel antibiotics (Schulze et al., 2015; Tian et al., 2016).
Incorporating software such as anti-SMASH (Blin et al., 2017),
THE IMPACT OF GENOMICS ON LACTIC PRISM (Skinnider et al., 2017) and GRAPE (Dejong et al.,
ACID BACTERIA 2016) has facilitated mining of the genomic data sets for crucial
biosynthetic gene clusters. A very similar process unlocks the
Genomic information has recently become essential when potential in genomic data sets of LAB. These microbes are capable
studying microbes in detail. These data sets can provide an of producing a wide variety of diverse anti-microbial peptides
immutable link to the organism that for the most part remains (Stoyanova et al., 2012; Zacharof and Lovitt, 2012). Capitalizing
constant. In well studied bacteria, such as many LAB, fully on these powerful analysis tools can realize much of the potential
sequenced genomes are readily available in a variety of species that a genomic data set provides and determine many possible
(Chenoll et al., 2015; Inglin et al., 2018). These may be used functions available to the bacterium in question. Researchers
as reference genomes when assembling draft genomes of the can forgo the culture based issues with screening for novel
strain at hand. Mining these genomes alone reveals information anti-microbial compounds and instead direct future experiments
on all traits available to the microbe. Potential products are more accurately. This process was adeptly demonstrated by
inferred from the genetic code and viable pathways can be Singh S. et al. (2015), to identify putative bacteriocins (Singh N.P.
determined analyzing the relevant genes. These pathways are et al., 2015). Twenty LAB genomes were assessed for relevant
categorized by their overarching function e.g., carbohydrate bacteriocin producing genes. Putative operons were identified
utilization pathways. Comparative genomic analysis between the leading to further characterization of novel bacteriocins. This
generic pathways available to LAB and the strain of interest simplistic process describes the exploitation of genomic material
may highlight the unique functional capacity of the particular to identify these traits of interest.
strain of interest (Makarova et al., 2006). De novo construction of The utility of genomic information is on the cusp of a
genomic information is also possible. Knowledge of characteristic generational leap forward. Third generation sequencers, such

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O’Donnell et al. Multi-Omics Technologies for LAB

as the Sequel II and the MinIon, are set to remedy many of This approach holds significant promise for several reasons,
the intrinsic issues associated with second generation sequencers primarily due to its potential to decipher cellular differences
(Rhoads and Au, 2015; Lu et al., 2016). These are primarily within heterogenous cell populations in any tissue or cell
a GC bias in fragmentation and amplification (Grokhovsky culture. Determining cell heterogeneity is an essential step
et al., 2011; Poptsova et al., 2014), short reads resulting in in understanding the development, regulation and response
difficult to sequence repeat regions (Bovee et al., 2007; Aird to external influence in a population of cells. This natural
et al., 2011; Genovese et al., 2013) and substantial burdens on heterogeneity is amassed and averaged in bulk sequencing
computational rearrangement of genomes from a huge volume approaches. Traditional sequencing removes much information
of short reads (Aldrup-Macdonald and Sullivan, 2014; Sims et al., that may indicate more nuanced reasons for phenotypes of
2014). Limitations associated with short read sequencing become interest. Many techniques have been developed to isolate and
apparent when analyzing large insertion sequences (Iranzo et al., sequence these single cells in a cost effective and high throughput
2014) or substantial rearrangements in chromosomal or circular manner (Wang and Navin, 2015; Lan et al., 2017; Hwang
genomic sequences (Darling et al., 2008; Sobreira et al., 2011). et al., 2018). Microfluidics and Fluorescent Activated Cell Sorting
Transposable elements often contain genes of interest encoding (FACS) are the most popular methods to date. FACS relies
traits such as antibiotic resistance and bacteriocin production on tagging and isolating fluorescent cells by capitalizing on
(Klaenhammer, 1993; Toomey et al., 2009). In some cases, critical the charged nature of a fluorescently tagged cell (Gross et al.,
processes such as genome replication are also intrinsically linked 2015). Microfluidics focuses on the precise combinations of oil,
to the presence of inverted repeats (El Kafsi et al., 2017) and surfactants and cells to create a droplet containing a single cell
structure variants of large genomic transfers between species (Lecault et al., 2012). These techniques are used in a variety of
often harbor crucial mechanisms (Kant et al., 2011). Progress fields and are perfectly designed for use in single cell sequencing.
in this area will have a significant impact on determining some Furthermore, these techniques are adapted to include lysing of
of the poorly understood traits associated with LAB (Teusink cells and to incorporate sequencing materials within the droplets
and Molenaar, 2017). Similarly, it will be possible to shed more encapsulating the cell components.
light on up-and-coming areas for LAB such as discovering novel Single cell sequencing technologies have focused on human
bacteriocins (Perez et al., 2014). The ability to analyse far greater cells to date. This is in part due to the ease involved in lysing them
read lengths (>20 kb) has facilitated the characterization of to release nucleic acids, enabling high throughput protocols.
clusters coding resistance to crucial antibiotics as well as accurate This issue is being addressed to link higher throughput cell
tracking of large translocations of patho-adaptive traits from isolation methods, such as microfluidics, including suitable lysing
commensals to pathogenic bacteria in the microbiota (Huang protocol for bacterial cells (Liu et al., 2018). For this reason,
et al., 2016; Proença et al., 2017). LAB are likely to have gained however, LAB studies availing of high throughput analysis are
traits from similar translocation events. not presently available. Despite this, proof of principle studies
However, this is the proverbial tip of the iceberg regarding demonstrate the potential for LAB research in this area. Large
the potential impact on LAB due to third generation sequencing. sequencing attempts to explore the “microbial dark matter”
The most striking example of this is the extraordinary amount of unknown areas of the tree of life (Rinke et al., 2013) in
of information in the form of epigenetics that is lost due to microbiome samples have been conducted. In a similar manner,
the fragmentation and sequencing process in next generation single cell isolation techniques may also be employed to analyze
sequencing. Epigenetic, post transcriptional modifications exert the least abundant bacterial species within community samples.
significant control on bacterial genomes resulting in altered Minor community members have been observed within the
phenotypes (Goldberg et al., 2007). Currently, there is a fermented dairy product Koumiss using this approach (Yao et al.,
significant cost in both time and money associated with 2017). The protocol, described by Yao et al., 2017, involves
determining epigenetic marks (Kurdyukov and Bullock, 2016; diluting microbiome samples and sequencing single cells. This
Soto et al., 2016). Both Nanopore and PacBio report the powerful, yet simplistic, technique can be exploited to analyze
presence of epigenetic modifications during sequencing (van Dijk pools of bacteria that are known to have a specific output or
et al., 2018). This will result in regular sequencing reporting phenotype in order to isolate the cells responsible. Analyzing
epigenetic alterations to bases, in turn opening this added layer of minute quantities of DNA and RNA, sometimes as low as
complexity to a far greater audience (Casadesús and Low, 2006). femtograms of material, are within the remit of these single cell
techniques (Lasken, 2007). This knowledge has been utilized in
environmental samples to isolate microbes of interest such as
OVERVIEW OF OMICS TECHNOLOGIES oil degrading microorganisms (Mason et al., 2012). Furthermore,
single cell segmented filamentous bacteria were isolated using
The following section will review the existing omics technologies microfluidics from mouse gut microbiome samples (Pamp et al.,
in the context of LAB. The advantages and disadvantages of each 2012). This protocol provides an isolation method applicable for
is summarized in Table 1. single cell LAB in community samples. Despite the lack of single
cell sequencing studies on LAB, many of the techniques described
Single Cell Genomics are directly applicable to LAB. These highlight the potential
Single cell sequencing approaches have become more frequently advances that are attainable in this area. The rapid progress of
utilized throughout the past decade (Tang et al., 2009). isolation technologies, lysing protocols and sequencing depth will

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TABLE 1 | Strengths and weaknesses of the individual omics technologies described in this review.

Data set Strengths Limitations Recent advances Citations

Genomic Immutable link to the organism; Short read sequencing results in gaps Third generation sequencing; simultaneous Bovee et al., 2007;
databases of reference in “hard to sequence” regions; epigenetic determination with genome Sims et al., 2014; van
genomes often available to aid impossible to determine the activity of sequencing; higher throughput for shotgun Dijk et al., 2018
reconstruction; provides a the genetic elements sequenced; meta-genomics
static image of genes of difficult reconstruction of genomes with
interest; high throughput bioinformatic software
sequencing as standard
Transcriptomic Robust data on the RNA isolation and sequencing are Higher throughput Next Gen Sequencers Lohse et al., 2012;
requirements of a microbe in a susceptible to handling errors; the (NovaSeq 6000); meta-transcriptomics of Vogel and Marcotte,
given environment; vast transient nature of RNA only provides a large systems is now possible; more reliable 2012; Liu et al., 2016;
quantity of data is produced; snapshot of the needs of the software for integration and variant Dagogo-Jack and
effective combination with organisms; presence of RNA’s does not determination Shaw, 2018
single cell technologies necessarily predict the translation into
proteins
Proteomic Significant database of known Throughput capabilities of proteomics Orbitrap Mass Spec facilitates ionization of Pascal et al., 2008;
proteins provide a strong lags behind other omics; expensive MS more complex proteins; combining liquid Michalski et al., 2012;
platform to predict function; machinery is required for proteomic chromotography with multiple MS’s allows The Uniprot
robust link between an research; concessions are made in accurate depiction of specific groups of Consortium, 2014; Ting
organisms proteomic profile order to analyze the vast array of proteins; powerful analytical tools i.e., et al., 2017; Monaci
and its phenotype; provides a proteins – Splitting large proteins into PECAN, facilitate more accurate predictions et al., 2018
more stable image of the smaller sections to facilitate MS analysis from untargeted proteomics
current requirements of the
organism than other omics
technologies
Metabolomic Direct connection between The transient nature of metabolites Back to back LC or MS machines provide Wang et al., 2014;
phenotype and metabolomics makes them susceptible to sampling higher resolution of specific groups e.g., Chetwynd et al., 2015;
profile; provides an image of artifacts; numerous costly LC/GC and LC-MS/MS; new machinery such as High Rebollar et al., 2016;
many well-studied metabolites MS machines needed for processing Temperature-Ultra High Performance LC Ferrocino and Cocolin,
simultaneously; diverse range are overcoming previously difficult to detect 2017; Zhang and
of applications across many metabolites; single cell sorting advances Vertes, 2018
fields are facilitating robust single-cell
metabolomics in the near future

The recent advances in their respective fields are included to illustrate the frequent progress in this area. As discussed below, many of the weaknesses that are mentioned
may be overcome by integration of several of these omics technologies together.

provide a more stable platform for targeted single cell analysis of omics data unveils a more dynamic image of the metagenome.
LAB (Gawad et al., 2016). This is most commonly applied when integrating genomic
and transcriptomic data. These data can be indispensable to
Metagenomics understanding the functional role members fill in a given system.
In contrast to single cell genomics, metagenomics provides
community-based genome sequences of many diverse species
simultaneously. This information allows correlation-based work COMBINING TRANSCRIPTOMICS WITH
to compare the abundance of particular gene families to the GENOMIC DATA SETS
respective environment (Brown et al., 2011). Metagenomics
provides an overview of species abundance in the microbiome The combination of genomics and transcriptomics is one
and characterizes common metabolic pathways available in of the most common in addressing experimental questions.
the ecosystem (Huttenhower et al., 2012). The contribution Combining transcript data with available genomic information
LAB make to the gene pool and functional processes can be provides an image of the intentions of the organisms, given a
discerned using metagenomic data. Armed with this knowledge, specific environmental situation. The integration of genomic and
the potential role LAB play in the community can be determined. transcriptomic data (Curtis et al., 2012; Ju et al., 2012; Craig et al.,
Metagenomics is regularly used to determine the microbial 2013; Lappalainen et al., 2013) is frequently used across many
diversity in order to direct further analysis of the sample at fields, while merging metagenome and metatranscriptome data
hand. Zhang et al., 2016, used metagenome sequencing to study (Shi et al., 2010; Solbiati and Frias-Lopez, 2018) is becoming far
novel fermented foods. These insights into fermented foods more prevalent. Genomic and transcriptomic data sets have been
revealed potentially interesting Lactobacillus strains that were combined regularly to offer insight into the role LAB play in
then isolated from the samples (Zhang et al., 2016). This targeted food spoilage (Andreevskaya et al., 2015), potentially probiotic
approach to omics data is the most effective method when traits of LAB strains (Saulnier et al., 2011) and their ability to
working with a single omics set. However, combining other use alternative electron acceptors in order to respire instead of

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O’Donnell et al. Multi-Omics Technologies for LAB

ferment (Brooijmans et al., 2009). Isolating strains with particular a greater opportunity to isolate mechanisms that stimulate
functions is readily facilitated by transcriptomics data. A systems desired responses (Hidalgo-Cantabrana et al., 2012; Shalek et al.,
approach was used to analyze the altered functional capacity 2013). This method is also efficacious when the genome and
of a mutated Lactococcus lactis strain utilizing genomic and transcriptome sequencing are carried out simultaneously on the
microarray data (Chen et al., 2015). The genetic component same cell (Macaulay et al., 2015). These researchers sequenced
responsible for its increased thermo resistance was determined the DNA and RNA of single mammalian cells in parallel,
using this combination of omics data. Transcriptome analysis demonstrating the current capacity of single cell technologies.
of Lactobacillus strains causing beer spoilage was performed to A subpopulation of 10% within 172 single cells of human
determine the functional pathways which enable these microbes and murine origin was reported after analysis. Several genetic
to enter the viable putative non-culturable (VPNC) state and alterations between cells and large chromosomal translocations
thus survive in beer. Analysis of three Lactobacillus acetotolerans events were observed.
strains revealed that these strains were in a heightened stress LAB are among the best understood constituents within the
state and had reduced gene expression levels in several other microbiome. However, it is difficult to determine the importance
regular pathways such as metabolic processes, transport and of their role in an ecosystem this large without a systems
enzyme activity. Understanding this process may afford future approach (Pessione, 2012; Waldor et al., 2015). Constituents of
opportunities to prevent beer spoilage by inhibiting entry into the the microbiome are known for their ability to affect the impact of
VPNC state (Liu et al., 2016). drug compounds and therapy (Lindenbaum et al., 1981), ferment
Fundamental processes in LAB such as amino acid and convert many components in our diet (Albenberg and Wu,
and carbohydrate metabolism have been advanced using 2014) and have significant impact on healthy brain function
transcriptomic data. Comparative transcriptomics has been (Foster and McVey Neufeld, 2013). Single cell technologies
imperative in understanding amino acid metabolism in may lead the way in deciphering LABs role in these functions
Lactococcus lactis MG1363. A codY mutant strain was used to of the microbiome.
determine the role this gene plays in regulating more than 30
genes involved in metabolizing amino acids (den Hengst et al., Metatranscriptomics
2005; Guédon et al., 2005). This strain was further analyzed using Advances in next generation sequencing technology have
transcriptomic data to analyze its global regulatory networks reached a sequencing depth that facilitates more comprehensive
during growth in milk (de Jong et al., 2013). Knowledge regarding metatranscriptomics of large community samples such as the
the expression of critical genetic components in LAB such as gut microbiome (Bashiardes et al., 2016; Furnholm et al.,
the catabolite control protein A (CcpA) has seen considerable 2017; Mehta et al., 2018). The current NovaSeq can produce
advancement using transcript data. Deep transcriptomic and 20 billion reads in a machine run. With this volume of
physiological data were used to explore the differential expression reads between 100–400 taxa can reach maximum saturation
between WT Lactobacillus plantarum and a CcpA mutant during of reads required for the highest statistical power (Ching
growth phase on different carbohydrates (Lu et al., 2018). This et al., 2014). This step forward provides a powerful tool for
study reports a substantial rearrangement in the carbohydrate gut microbiota analysis and realizes a true systems biology
metabolism regulatory network and sheds new light on the approach to determining how this community reacts to
complexity of this process. It is clear that incorporating this environmental perturbations. Due to the large database of
data set into LAB research has already led to an increased sequenced LAB genomes, LAB stand to gain the most from
understanding of these microbes. the analysis of ecosystems such as the gut microbiome with
a systems level approach. This combination of metagenomics
Single Cell Transcriptomics and metatranscriptomic data is just beginning to become
Transcriptomics at a single cell resolution is a relatively new relevant in larger ecosystems; however, significant results have
field that may unravel many of the changes in transcription already been attained.
that are altered through a cells life span. These alterations To date, this approach has been observed in smaller
are completely masked by bulk transcriptomics (Shapiro et al., microbiome samples such as Kimchi (Jung et al., 2013) and
2013). With new technologies providing faster delineation of rumen (Kamke et al., 2016). This methodology was also used
single cells (Klein et al., 2015) in conjunction with greater in a proof of principle analysis to determine the function of
sequencing depth with machines such as the NovaSeq, large a critical microbe in bacterial vaginosis. Indeed, by utilizing
scale single cell transcriptomics is more accessible than ever. metatranscriptomics Lactobacillus iners was implicated in having
Progress in these complimentary fields allows researchers to a functional role in the presence of this disease differentially
explore a previously unavailable aspect of cell state heterogeneity. expressing over 10% of its genome between healthy and disease
Many single cell transcriptomic studies focused on stem states (Macklaim et al., 2013). Specific commercially important
cells (Kolodziejczyk et al., 2015), embryos (Yan et al., 2013), processes such as cheese ripening have also seen the impact
tumors (Patel et al., 2014) and the nervous system (Zeisel of this approach. Despite using shallower metatranscriptome
et al., 2015). The use cases for this approach in these tissue data, De Filippis et al., 2016 demonstrated temperature-driven
types are apparent due to the advantages of delineating functional changes in the cheese microbiome during ripening
the differences between differentiated and non-differentiated which had a significant impact on cheese maturation rate.
cells. Comparing the responders to non-responders provides They indicated that “processing-driven microbiome responses”

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can be altered to influence product quality and production sets. Despite considerable advances in proteomic technologies of
efficiency (De Filippis et al., 2016). Expression data that can late (Michalski et al., 2012; Hein et al., 2013; Gillet et al., 2016),
be tracked throughout the process and related back to the this omics data set is the limiting factor in relation to throughput
specific strains responsible is invaluable in important commercial when integrated with genomics and transcriptomics. Untargeted
processes such as cheese production. The potential to carry discovery proteomics is termed Data Independent Acquisition
out similar research in large microbiome samples such as (DIA) and allows the most comprehensive combination with
the gut, in a manner similar to De Filippis’ experiment, is other omics sets (Hu et al., 2016). This process facilitates
fast approaching. the tracking of genes to proteins in a manner that produces
Third generation sequencing platforms may have a direct functional data (Tocchetti et al., 2015; Trapp et al., 2016;
impact on the RNA-seq field. Long read technologies perform Kedaigle and Fraenkel, 2018).
better in the determination of unknown transcript abundance Protein abundance is intrinsically linked to the mRNA levels
in single celled organisms (Tombácz et al., 2018), full-length discussed above, however, mRNA abundance does not correlate
splice isoforms with alternative splicing (Xu et al., 2017) and well to protein abundance in a system (Chen et al., 2002;
co-transcription of genes in a polycistronic fashion (Tardaguila Pascal et al., 2008; Vogel and Marcotte, 2012). Considering
et al., 2018). It is clear that there are obvious advantages this disparity, and that proteins are the molecules that control
to long read sequencing in reducing the difficult reassembly almost all cellular processes, the benefit from integrating these
and loss of contextual information associated with short read technologies for a more complete image is clear (Griffin et al.,
sequencing. However, the lower accuracy and sheer scale of some 2002; Cox and Mann, 2007). When combined, these data sets
transcriptomics and metatranscriptomics projects keeps them can answer higher dimensional questions about large scale
out of reach of current third generation sequencers. processes such as studying the metabolism of many products
Integrating metatranscriptomics with deep metagenomic data simultaneously in a holistic manner (Delmotte et al., 2010;
presents the ability to track a time mediated response to specific Wang et al., 2013). Complex microbial interactions such as
changes in the environment. Be it antibiotic exposure, pathogenic quorum sensing may be deciphered using this approach (Di
infection or probiotic administration, a wealth of information on Cagno et al., 2011). This process was carried out to assess the
how the system is reacting to the alteration will be generated. complex interplay between LAB strains in yogurt fermentations.
Such data could be tracked back to each species and provide Transcriptomics and proteomics were combined to understand
information on how to produce effective therapies in similar how the strains present interacted to produce the desirable effects.
situations. This holistic approach to studying these bacteria in By-products from a single strain stimulated growth in the co-
their natural habitat will reveal much about the production of culture resulting in a reliable yogurt formation (Herve-Jimenez
compounds of interest and may result in interesting revelations et al., 2009; Sieuwerts et al., 2010). Similarly, this information
about the transition between the microbiomes symbiotic and can be used to further understand specific traits of LAB such as
dysbiotic states. their crucial ability to manage bile stress in the case of probiotic
strains of Lactobacillus (Koskenniemi et al., 2011). Combining
proteomics with genomics and transcriptomics allows more
ASSESSING THE UTILITY OF robust biomarkers and treatments to be determined. This is
PROTEOMICS WITHIN MULTI-OMICS observed in traits of disease phenotypes in humans (Wheelock
DATA et al., 2013) or functional processes in bacteria (De Keersmaecker
et al., 2006). Understanding the methods that bacteria use
Proteomics investigates the complete set of proteins present to interact with their environment through several omic data
in a cell, tissue or organism at a molecular level. Proteomics sets develops network links between these data sets. Primary
in its own right is a powerful analytical tool that has helped processes such as stress responses are frequent targets for a
resolve many functional questions regarding LAB. Proteomic combinatory approach and may reveal critical information that
analysis has determined abundant compounds that are present would be lost without a holistic approach (Dressaire et al., 2011).
in the transition between growth phases in LAB (Pessione et al.,
2005) and has been used to study the metabolic interactions Single Cell Proteomics
of LAB (Pessione et al., 2010). Proteomics has determined Single cell analysis also makes an impression on the field
critical proteins involved in acid stress resistance in Lactobacillus of proteomics. Until recently, there were merely proof of
casei comparing a known stress resistant mutant to the Wild principle publications describing the ability to identify minute
Type (WT) strain (Wu et al., 2012). Assessing the complete set concentrations of proteins available in a single cell (Jo et al.,
of secreted proteins in LAB has increased our understanding 2007; Rubakhin and Sweedler, 2007). Mass spectrometry, the
of how these bacteria interact with their environment (Zhou primary method for proteomics research, is frequently used
et al., 2010). Research to determine the capacity for LAB when tens of thousands of cells are available from which to
to resist osmotic stress, a critical trait of all microbes in extract proteins. However, a single cell has in the region of
challenging environments, has also progressed notably utilizing 1 × 105 protein molecules. With this in mind, it is clear
proteomics (Zhang et al., 2010). These examples serve to prove why single cell mass spectrometry (MS) techniques will reveal
the flexibility and effectiveness of proteomics; however, this only the most abundant of proteins present. Despite this,
information is best used when combined with other omics data advances in this area have increased the scope of single cell

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O’Donnell et al. Multi-Omics Technologies for LAB

proteomics considerably. Progress within the flow cytometry this process to incorporate gut microbiome samples is beyond
field has resulted in an increased variety of fluorescent markers current proteomic technologies (Verberkmoes et al., 2009).
(Krutzik and Nolan, 2006). Antibody based immunofluorescence
confocal microscopy has been used in human cells to identify
>12,000 proteins across multiple cell lines (Thul et al., 2017). COMPLETING THE MULTI-OMICS
Microfluidic image cytometry can now analyze activity of specific PICTURE: METABOLOMICS
protein groups such as kinases (Sun et al., 2010) and using
photocleavable DNA barcode-antibodies to quantify various Metabolomics is the study of all metabolites produced in a given
proteins from single cells is also possible (Agasti et al., 2012; system. This omics technology is a natural progression from
Ullal et al., 2014). These techniques have enabled targeted proteomics in that proteins are responsible for the presence of the
proteomics of single cells, however, to our knowledge no single majority of metabolites found in an organism. The far-reaching
cell proteomics work has been carried out on LAB. Tracking the effect that metabolomics research may have is apparent, as all
mechanisms and rate at which single cells adapt to environmental phenotypes are intrinsically linked to the metabolites involved
exposures will help define the specific triggers, systems and in the system studied. This concrete connection between the
pathways involved in these situations. Developing knowledge of phenotype and metabolome makes it an exciting data set to add
these networks while avoiding the clouded nature of bulk analysis to any research. The volume of information that can be gathered
is the most effective method to increase the accuracy at which we is substantial considering the sheer scale of all metabolites that
can predict the function and reactions of these microbes. may be present. Recent advances have resulted in more accurate
systems than ever for delineating these compounds. Back
Metaproteomics to back Liquid Chromotography or Mass Spectrometry units
Currently, meta-proteomics struggles to stack up (LC/LC-MS, LC-MS/MS) (Cui et al., 2018), High Temperature
to the comprehensive nature of metagenomics and Ultra High Performance Liquid Chromotography (HT-UHPLC)
metatranscriptomics. However, a recent study by Ting et al. (Yoshida et al., 2007; Sarrut et al., 2014) and nanoflowUHPLC-
(2017) depicts the current power of untargeted exploratory nanoESI-MS (Chetwynd et al., 2015) are filling in the gaps for
proteomics accurately. This group demonstrated that the previously difficult to detect compounds such as hydrophilic
difference between the more comprehensive nature of Data or minor metabolites. This progress results in untargeted
Independent Acquisition and more accurate Data Dependent metabolomics reaching the throughput necessary to combine
Acquisition (DDA) is lessening. After developing a novel library them comprehensively with other omics data sets.
free peptide detection method, PECAN, this group was capable The utility of metabolomics technology on its own is
of detecting 12,767 peptides within a sample, 6,221 of which were obvious and has been used to make connections between gut
unique compared to the targeted approach. The untargeted DIA related diseases and metabolites produced by gut microbes
approach detected 83% of the peptides elucidated during the (Bingham, 1999; van Nuenen et al., 2004; Nicholson et al., 2005).
targeted DDA approach. The detection accuracy was impressive Metabolomics has also been utilized to decipher functions of
as ∼99.5% of the retention times were identical between both LAB such as their role in commercially important processes and
approaches. This is while simultaneously detecting more than revealing information regarding their metabolism (Weckx et al.,
twice the number of peptides, indicating its suitability for 2010; Wilson et al., 2012; Mozzi et al., 2013). In a study by Hong
exploratory proteomics. Techniques such as this are facilitating et al., 2011, probiotic LAB were introduced to a group of Irritable
more realistic, high throughput proteome analysis (Kim et al., Bowel Syndrome (IBS) sufferers. NMR was used to determine the
2014). This represents the future of larger scale metaproteomic metabolic niche that these LAB fulfilled in the IBS sufferers by
work; however, it is still in its infancy. For this reason, targeted comparing them to a control group not receiving the probiotic
assessment of protein abundance and identification is more (Hong et al., 2011). The resulting data suggested a dysregulation
appropriate and useful than untargeted in its current state. As in energy homeostasis and liver function based on the metabolites
such a targeted approach must often be taken when combining present. The potential of metabolomic data sets are unlocked
the information with metagenomic and metatranscriptomics when linked to other components throughout the organism such
data. It is feasible to choose a specific function or set of functions as proteins, RNA etc.
to analyze as part of the system-wide metaomics approach. Many functions have been determined integrating these data
Important traits associated with functional features of LAB sets as they provide a powerful platform to answer many research
can be interrogated further with proteomics in this manner questions. This has been observed in several fields such as
(Hamon et al., 2011; Perez Montoro et al., 2018). Analyzing chemotherapy toxicity, toxicology, fungal phytopathology and
functional traits has developed a significant understanding of heavy metal resistance in plants (Heijne et al., 2005; Tan et al.,
the proteome of the LAB group to date (De Angelis et al., 2016). 2009; Singh S. et al., 2015; Wilmes et al., 2015). In LAB,
Several studies in 2019 have combined metaproteomic data this combination of technologies is useful when analyzing an
sets with the genomic counterparts to analyze fermented foods. organism-wide response such as growth efficiency and amino
This phenomenon has revealed much information regarding acid metabolism (Lahtvee et al., 2011) or the ability to adapt to
the central role played by LAB in these functional foods (Xie ecological niches (Heinl and Grabherr, 2017). Conversely, these
et al., 2019a,b). However, these metaproteomic approaches omics can be used with a specific end point in mind such as
may only assess smaller scale community samples. Expanding probiotic potential to treat a specific issue, providing a powerful

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O’Donnell et al. Multi-Omics Technologies for LAB

protocol for selecting suitable candidates (Rebollar et al., 2016).

A combination of genomics, transcriptomics and metabolomics
has been used to analyze the microbial role in the fast growing
area of milk whey. Milk whey has recently transitioned from
a low value by-product to a high value commercial product.
However, the regulation has lagged behind resulting in many
unknowns regarding the microbial composition and microbial
by-products present in this milk whey. Omics data sets allowed
Sattin et al., 2016, to report the reasons for poor whey
quality, the potentially concerning compounds present and
how to maintain higher commercial value (Sattin et al., 2016).
Similar processes’ were described when assessing the role multi-
omics data may play in food microbial interactions (Sattin
et al., 2016; Ferrocino and Cocolin, 2017). Indeed, genomics,
transcriptomics and metabolomics aided Turroni et al., 2016, in
deciphering the complex interactions that allow Bifidobacterium
strains to persist in the murine gut (Turroni et al., 2016).
This valuable information leads to a greater understanding of
the functional requirements for probiotic strains to survive
this environment.
Exploiting multi-omics data sets is now a pivotal step in
discovering novel antibiotics (Palazzotto and Weber, 2018).
Albright et al., 2014, demonstrate a clear methodology for
screening strains for novel antibiotic metabolites based on multi-
omics data (Albright et al., 2014). Figure 1 shows a generalized
version of the method outlined in this paper. The flow begins
with sequencing the genome of the strain of interest. This
facilitates searching the genome for the presence of biosynthetic
gene clusters that may indicate antibiotic production. The
genome enabled proteomics used in this study produced >15
fold increase in the number of antibiotic peptides detected
compared to regular proteomic analysis. After determining the
relevant proteins produced, metabolites were assessed using data-
dependant acquisition. Metabolites associated with the proteomic
data set that represent potential antibiotic compounds are
selected for using LC MS/MS. Isolated metabolites are compared
to the relevant databases to rule out the known compounds. In
this manner, novel natural products are isolated in an effective
progression from strain to isolated compound using multi- FIGURE 1 | The flow chart depicts a generalized version of the methodology
omics data. used by Albright et al. (2014) to isolate novel secondary metabolites with
antibiotic potential.
Single Cell Metabolomics
Single cell metabolomics, although still in its infancy, can
reveal the closest link to the phenotype of a single cell in a Live single cell mass spectrometry shows promise providing
population. Sample volumes, low concentrations of analytes and rapid, direct analysis of targets while also producing a complete
sampling techniques are significant obstacles to this technology annotation of the results in less than one hour (Fujii et al.,
based on miniscule substances. However, in recent years, we 2015). Fluorescent based techniques relying on flow cytometry
have seen significant steps in accurate sampling of metabolites. and direct microscopy are suitable methods for analyzing
A comprehensive review has been completed by Duncan et al., specific metabolites (Li et al., 2016; Mondal et al., 2017).
2019, on the state of the art techniques developed over the last More recent developments in single cell technologies such as
three years for single cell metabolomics (Duncan et al., 2019). microfluidics are also applicable in isolating cells based on
A primary concern of these techniques is the transient nature their extracellular metabolite profile (Wang et al., 2014). With
of metabolites. A cell with particularly fast metabolic turnover associated technologies progressing quickly, it is clear that single
can change its metabolic profile in 0.3 s (Zhang and Vertes, cell metabolomics will make large steps with regard to throughput
2018). This volatility means the cells must be maintained in the and accuracy in the near future. However, no LAB based single
native environment and treated carefully to avoid artifacts of the cell metabolomics data are available in published literature.
sampling technique. Despite the difficulty in accessing the metabolomic data of single

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O’Donnell et al. Multi-Omics Technologies for LAB

cells, the utility of the information is clear. This analysis allows each of these approaches has limitations when negotiating
abundance of specific metabolites to be confidently linked to these data. These limitations manifest in difficulty transforming
traits. Moreover, developing specific links will aid functional differing data sets, combining massive input matrices and
prediction in all similar microbes with metabolomics data. over fitting training data. Most pipelines adopt one of these
The flexibility of these data sets is apparent and with the approaches as a broad starting point. Researchers will have
advent of more effective and comprehensive technologies, even nuanced differences in how they treat types of data and how they
more research will move to this culture independent, data driven weight connections between their data points.
approach. Further development in multi-omic databases will A creative use of a transformation based approach has led to
fuel research in improving the technologies related to each remarkable results in liver cancer survival prediction (Chaudhary
omics data set. Understanding the methods that bacteria use to et al., 2018). This model developed by Chaudhary et al., 2018 uses
interact with their environment through analysis of simultaneous a deep learning method autoencoder and a single variate cox-
omics data sets will result in the development of network PH model to choose features associated with survival. K-mean
links between the data sets themselves. Common links that clustering is applied to these features to determine survival-risk
are regularly observed between omics data sets will lead to groups. The omics data sets are then ranked via an ANOVA and
greater molecular understanding and will be incorporated into features common with the predicting set are chosen. This step is
traditional interaction networks. Extracting and depicting these depicted in Figure 2, where omics data sets are transformed into
complex interactions is an intrinsic issue associated with big data survival-risk predicting sets. These ranks can then be compared
sets that multi-omics produce. Complex software pipelines play and combined. The final survival-risk labels are generated from
an important role in making sense of these data. To this end, we the top features chosen by this method (Chaudhary et al.,
will briefly mention the more prominent software used for these 2018). By incorporating microRNA seq, RNA seq, methylation
integration processes. and genomic information this study highlights the potential
powerful use for multi–omics data when appropriate software
can realize its potential.
DATA INTEGRATION AND An R based software, mixOmics, presents a recent example
COMPUTATIONAL LIMITATIONS of a modified concatenation-based approach (Rohart et al.,
2017). This R based software uses its “Diablo” process for
The integration of data sets generated in multi-omics research is this approach. Diablo incorporates all the input variables into
by no means trivial. Each omics technology naturally consists of a single input matrix. During this process interactions and
different types of data complicating the analysis to begin with. associations between data sets are factored into the single
This is further complicated by the sheer volume of information input matrix. Figure 3 represents a schematic of this approach,
that must be sifted through, particularly with meta-omics data. combining the different omics sets while taking interactions
Software pipelines have been developed to manage this seemingly between data sets into account. This adds another level
impossible task. Programs are developed to create models that of complexity that suits multi-omics approaches specifically,
can predict outcomes when multi-omics data is inputted. The creating a more powerful input matrix from which the model
outcomes analyzed are frequently disease states that can be is derived. This software also contains another pipeline, namely
described in terms of multi-omic data sets using these techniques. “MINT”, which is a model-based integration where data sets
These pipelines generally fit into one of three approaches. of the same type, e.g., transcriptomics, from different studies
These models approach the issue with different methods, but are combined to produce a model. Each type of data set
all are valuable assets available to integrate the data. However, predicts aspects of the phenotype as illustrated in Figure 4. The

FIGURE 2 | Transformation based integration: Each omics data set is transformed into comparable input matrices. Relevant identifiers are united to build the
predictive model from all transformed data sets. This model discerns phenotypic traits that can be quantified using multi-omics data.

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O’Donnell et al. Multi-Omics Technologies for LAB

FIGURE 3 | Concatenation based integration: Omics data sets (colored rectangles) are combined at the beginning of concatenation based integration. Identifiers are
determined between and within each omics set. These identifiers are combined and used as a model to discern specific attributes within the phenotype.

FIGURE 4 | Model based integration: Each omics data set is used as a model to determine identifiers of traits within the phenotype. The phenotypic traits that are
discerned from each omics data set/model are weighted based on their capacity to predict the phenotype. These weighted identifiers are then combined and
ultimately predict the phenotype.

predictions determined by each model are weighted based on more types of omics data. These advances are essential to keep
their propensity to determine the phenotype. These input models up with the rapidly increasing volumes of data and to address the
are subsequently combined to generate a final prediction model current limitations associated with many original data sets (Pinu
(Rohart et al., 2017). et al., 2019). Several studies have emphasized the over estimation
These exciting new software packages encompass each of the of significant results and several contradictory outcomes in multi-
major methods of generating models for integrating omics data. omics data sets in many high impact publications (Ioannidis,
Many developers are constantly updating and upgrading their 2005; Ioannidis and Trikalinos, 2005). In these cases, genuine
platforms to incorporate the latest data sets and produce the heterogeneity within samples in genome wide association studies
most effective models (Medina et al., 2010; Alonso et al., 2015). is considered statistically important disease specific information
Many concatenation based approaches have been developed to (Ioannidis et al., 2003; Kavvoura et al., 2008). Software tools
address nuanced different data sets (Fridley et al., 2012; Kim must understand and incorporate these issues, while avoiding
et al., 2013). Cancer survival prediction has seen significant the risk of false negatives due to too harshly correcting data. For
success utilizing transformation and model based approaches. more information on the challenges associated with integrating
This progress has been observed using multiple genomic these data sets, the reader is directed to the following review
data sets to accurately assess ovarian cancer survival and in articles (Palsson and Zengler, 2010; Gomez-Cabrero et al., 2014;
predicting instigators of melanoma from gene expression data Fondi and Lio, 2015). For the reasons detailed above, there
and chromosomal copy number variation (Akavia et al., 2010; must be an element of responsibility on biologists to negate
Kim et al., 2013). some of these limitations by developing a workable level of
More powerful models are constantly being developed, understanding regarding the most suitable software model for
incorporating ever expanding data sets while integrating even their experimental questions.

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O’Donnell et al. Multi-Omics Technologies for LAB

CONCLUSIONS develop skills in data processing, develop an understanding of

the mechanisms behind software they utilize and be flexible
The mechanisms responsible for generating omics information to incorporating new technologies into their workflows. This
have seen considerable progress in recent years. The advent task is challenging, but the rewards available with multi-omics
of new technologies, such as third generation sequencing, are substantial.
is capable of transforming the level of information available
to researchers. These advances have placed the integration
of multiple omics data sets within reach of more scientists. AUTHOR CONTRIBUTIONS
This availability will result in substantial advances in all
aspects of microbial work from delineating specific functions SO drafted the initial manuscript. CS and RR provided critique
to understanding their role in complex ecosystems. This review and corrections and all worked together in the construction of
assesses the advantages to a high dimensional systems level the final review.
approach when analyzing organisms and systems simultaneously.
The fortuitous position that LAB research finds itself in is
also discussed. LAB are a group of microbes with a wealth FUNDING
of data already available in a variety of databases. Due to
this position, research focused on this group is poised to take We would like to acknowledge funding from the Department
full advantage of the progress in multi-omics research. As the of Agriculture, Food and the Marine, Ireland. Project
field of molecular biology becomes a data intensive one, it is Ref. No: 15 F 602, and in part by a research grant from Science
critical that biologists keep up with this trend. Researchers must Foundation Ireland under Grant Number SFI/12/RC/2273.

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profiling of human preimplantation embryos and embryonic stem cells. Nat. potential conflict of interest.
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