Table 1 ‘Omics’ techniques applied in studying probiotic and microbiome interaction.

Whole-genome sequencing

Limosilactobacillus reuteri PNW1

Determination of probiotic potential

• Genes encoding D and L-lactate dehydrogenases.

• Genes responsible for adhesion to epithelial tissues, including antiadhesion Pls, Sortase A, exopolysaccharide cluster,

• Genes encoding bioactive peptides (S-ribosyl homocysteine lyase, Autoinducer-2 production protein LuxS

• Four coding regions associated with enhancing host metabolism and enzymes such as Poly (glycerol-phosphate) alpha-glucosyltransferase.

²⁸

Metagenomics (Sequencing of V3-V4 region of the bacterial 16S rRNA)

Lactobacillus rhamnosus, Enterococcus faecalis

Determination of the effects of direct-fed microbes on the rumen microbiome of goats

• Showed the influence of direct-fed Lactic acid bacteria on the microbiota in goats

³⁵

Metagenomics (Sequencing of V3-V4 region of the bacterial 16S rRNA)

L. rhamnosus PT9, L. rhamnosus PT10

Determination of the effects of direct-fed microbes on the rumen microbiome of sheep

• Revealed the effects of the lactic acid bacterial administration on the ruminal microbiome of sheep

³⁶

Metagenomics (Sequencing of V3-V4 region of the bacterial 16S rRNA)

Saccharomyces cerevisiae boulardii CNCM I-1079 Lactobacillus acidophilus BT1386

Determination of the effects of directly fed microbes on calves’ ruminal microbiome

• Decreased in pathogenic and increased in beneficial bacterial populations, respectively.

• Impacts on pathways include cell cycle, bile secretion, proteasome, cAMP signaling, thyroid hormone synthesis, and dopaminergic synapse pathways.

³⁴

Transkingdom network analysis

Lactobacillus johnsonii and Lactobacillus gasseri)

Determination of probiotics on the liver functions

• Attenuation of western diet-induced diabetes through the improvement of lipid metabolism and enhanced mitochondrial health.

⁴⁵

Transcriptomics

Lactiplantibacillus plantarum LIP-1

Determination of Lactiplantibacillus plantarum LIP-1 responses to different Ph

• Unraveled the microbe’s responses and enhanced the means to improve survival in a lyophilized state.

⁴⁶

Transcriptomics

Bifidobacterium breve UCC2003

Influence of B. breve UCC2003 on the intestinal barrier

• Described the functions of B. breve UCC2003 in intestinal epithelial homeostasis during early life in neonatal murine intestinal cells.

⁴⁷

Metatranscriptomics

yeasts and Lactobacillus species

The interplay of the microbes during the fermentation of

• Revealed the role of the probiotic microbes in pyruvate metabolism

⁴⁹

Metatranscriptomics

Oral microbiota

Interactions of the oral microbiome in biofilm biomass

• Unraveled the complex interactions of the oral microbiome in biofilm assembly

⁵⁰

Peptidomics and Metagenomics

Lactobacillus helvetius NS8 and Lactobacillus fermentum NS9

Determine the effects of the probiotics on the peptidome of specific pathogen-free mice

• Alters the hippocampus peptidome by acting on the gut-brain axis.

• No substantial alteration on the gut microbiome

⁵⁸

Shotgun metaproteomics

Gut microbiota

Revealed the response of the host to the microbiota

• Revealed human proteins and antimicrobial peptides

⁶⁰

Metabolomics and 16S RNA sequencing

Lactobacillus casei Zhang

Determined changes in the metabolic profile of L. casei Zhang culture

• Revealed changes in several metabolic pathways including amino acid and carbohydrate metabolism.

• Showed the metabolic changes associated with glucose restriction to strain.

⁶⁹

Metabolomics

Lactobacillus plantarum MLK 14-2, L. plantarum KCCM 11322

Determined the variations in the metabolic changes in kimchi during fermentation with different strains

• Revealed the applications of metabolomics to monitor the fermentation characteristics of the strain.

• Showed that the metabolites vary with the starter culture strain used

⁷¹

Metabolomics

Lactobacillus plantarum NCU116

Determined the effects of ingesting L. plantarum NCU116 on the metabolite profile of hyperlipidemic rat model fed high fat diet

• Revealed biomarkers associated with high-fat diet in the serum of the model experimental animal.

• Showed the biological pathways and functions associated with the metabolites.

• Improvement in the hyperlipidemic condition of the rat via biosynthetic and metabolic pathways.

⁷⁵

Metabolomics

Lactobacillus paracasei subsp. paracasei SM20 and Propionibacterium jensenii SM11

Studied the antiyeast activities of the strains against Candida pulcherrima and Rhodotorula mucilaginosa

• Antiyeast compounds resistant to proteinase K and pronase E treatments were detected.

• Other low molecular weight compounds that play role in the complex antiyeast activities were also identified

⁷⁶

Metabolomics

Lactobacillus rhamnosus GG

Determine the effects of supplementing L. rhamnosus GG as a probiotic in alcoholic liver disease induced rats

• Normalized the level of fatty acids in the liver and feces of alcoholic liver disease induced rats.

• Prevents alcoholic liver disease in the treated rats.

• Modifies the gut microbiome to stimulate the synthesis of long chin fatty acids.

• Elevates the level of some essential amino acids through amino acid biosynthesis.

⁷⁷

Lipidomics coupled with RT-PCR gene expression

Multi-strain probiotics VSL#3 and IT-3 (containing different strains of lactobacilli, Bifidobacterium and Streptococcus thermophilus)

Determine the lipidemic response of Caenorhabditis elegans to different probiotics preparations.

• Variation in the lipid contents C. elegans fed VSL#3 compared to IT-3.

• Positive correlation between the genes encoding the fatty acid and the levels of the respective lipids.

⁸²

Lipidomics

Lactobacillus plantarum APsulloc 331261

study the extracellular vesicle phospholipid of the strain

• Variation in the phospholipid level between the extracellular vesicle and the parent cells

• Revealed high level of phosphatidylcholine synthase and lipopolysaccharide which could be used as biomarkers for clinical applications

⁸³