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Keywords:

  • Lactobacillus acidophilus ;
  • food microbiology;
  • probiotics;
  • taxonomy;
  • genomics;
  • identification

Abstract

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Lactobacillus acidophilus is a commercially significant bacterial probiotic, originally isolated from the human gastrointestinal tract and designated Bacillus acidophilus in 1900. Throughout the development of methods to identify and characterise bacteria, L. acidophilus has undergone multiple taxonomic revisions and is now the type species of a phylogenetic subgroup in the highly diverse and heterogeneous Lactobacillus genus. As a result of the limitations of differentiating phenotypically similar species by morphological and biochemical means and revisionary nature of Lactobacillus taxonomy, the characterisation of L. acidophilus has struggled with misidentification and misrepresentation. In contrast, due to its global use as a probiotic supplement in functional foods, L. acidophilus sensu stricto is now one of the most well-characterised Lactobacillus species. Here, we establish the provenance of L. acidophilus strains, unpicking historical and current misidentifications of L. acidophilus, and reviewing the probiotic, genomic and physiological characteristics of this important Lactobacillus species.


Introduction

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Lactic acid bacteria (LAB) constitute a diverse group of Gram-positive, nonsporulating, catalase-negative organisms that are found in a number of habitats (Carr et al., 2002). LAB comprise multiple genera within the order Lactobacilliales that are acid tolerant, of which Enterococcus, Streptococcus and Lactobacillus species are among the most well characterised. They are known constituents of the human gut (Arumugam et al., 2011) and also occur widely in dairy, meat, plants and fermented products of commercial value (Carr et al., 2002). As a result of their ancient anthropological use in food preservation and their ability to rapidly ferment carbohydrates to lactic acid, they have become industrially important bacteria and are used in a myriad of food and agricultural fermentations worldwide. Their growth causes acidification of food material, preserving the product and imparting unique textures and flavours (Kleerebezem & Hugenholtz, 2003).

Probiotics are ‘live microorganisms which, when administered in adequate amounts, confer a health benefit on the host’ (FAO/WHO, 2002). Lactobacillus acidophilus is widely recognised to have probiotic effects and is one of the most commonly suggested organism for dietary use (Shah, 2007). It is frequently added to yoghurt and fermented milk products, with c. 80% of the yoghurts produced in the United States containing L. acidophilus (Sanders, 2003). Lactobacillus acidophilus isolates also form part of the natural human microbiota and have been cultured from the oral (Ahrné et al., 1998), digestive (Kulp & Rettger, 1924) and vaginal (Rogosa & Sharpe, 1960) tracts. Here, we summarise key research on L. acidophilus, spanning its original isolation as normal human microbiota (Fig. 1) and describing its genomic, biosynthetic and probiotic characteristics (Fig. 2). In addition, we emphasise a need for rigour in describing L. acidophilus isolates by highlighting recent studies that incorrectly report the identity of isolates.

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Figure 1. History of Lactobacillus acidophilus. Major milestones in the development of Lactobacillus taxonomy, and the resulting effects on the taxonomic placement of Lactobacillus acidophilus.

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Figure 2. Major genomic, biosynthetic and probiotic characteristics of Lactobacillus acidophilus. Historically, Lactobacillus acidophilus has been known for its probiotic effects in humans. Through further characterisation of this effect, and the determination of the genome sequence of Lactobacillus acidophilus NCFM, many biosynthetic capabilities of Lactobacillus acidophilus have been described.

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Taxonomy of the lactobacilli

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Lactobacillus is a highly heterogeneous genus, encompassing bacteria with a wide range of biochemical and physiological properties (Felis & Dellaglio, 2007). The genus Lactobacillus is the largest of those that belong to the LAB, with 185 species validly described at the time of writing, and increasing substantially from 145 in 2008 as a result of the reclassification of multiple species (Euzéby, 1997; Claesson et al., 2008). From the initial description of the species Lactobacillus acidophilus in 1920 (Holland) until around 1970, many Lactobacillus isolates from human mucosal surfaces were collectively identified as L. acidophilus (Fig. 1). The identification of isolates using traditional phenotypic characteristics such as the fermentation of carbohydrates and cellular morphology, combined with the lack of a robust taxonomical framework, had historically led to such Lactobacillus isolates being incorrectly designated at the genus and species level. At the last review, the taxonomy of the genus Lactobacillus, it consisted of 14 phylogenetic subgroups (Felis & Dellaglio, 2007).

The L. acidophilus group is one of the most well-defined and deep-branching Lactobacillus phylogenetic subgroups (Fig. 3). Although its definition is partially based on DNA-DNA homology, the genomic GC content of constituent species ranges from 32% to 50% (Felis & Dellaglio, 2007), which is much larger than normally accepted for well-defined bacterial genera (Schleifer & Ludwig, 1995). The dawning of the postgenomic era has now added more tools to the taxonomist's toolkit, providing clarification and as well as further insight into how the taxonomy of the most challenging and complex bacterial groups can be resolved. Recent research into the relatedness of species in the L. acidophilus group has used polyphasic taxonomy, combining traditional phenotypic characteristics, such as sugar fermentation patterns (Yeung et al., 2004), sequence analyses of genes, such as 16S rRNA, rpoA, pheS (Naser et al., 2007), groEL (Claesson et al., 2008), tuf (Ventura et al., 2003), DNA fingerprinting methods such as rep-PCR (Gevers et al., 2001) and pulsed-field gel electrophoresis (PFGE; Yeung et al., 2004). These analyses have shown remarkable congruence with genome microarrays and genomic sequence comparisons, indicating that the L. acidophilus phylogenetic subgroup is a natural bacterial group. Genome sequencing now offers a definitive means to identify Lactobacillus species and strains (Claesson et al., 2007, 2008; Felis & Dellaglio, 2007; Bull et al., 2012).

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Figure 3. Phylogenetic placement of the Lactobacillus acidophilus phylogenetic subgroup within the Lactobacillus genus. A phylogenetic tree of aligned 16S rRNA gene sequences from type strains of the Lactobacillus acidophilus phylogenetic subgroup (indicated with a brace) and representative type strains from the other Lactobacillus phylogenetic subgroups. The tree was rooted with the 16S rRNA gene from Bacillus subtilis DSM10. The genetic distance scale, bootstrap values and GenBank nucleotide accession numbers are indicated.

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Lactobacillus acidophilus strains and their history

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Within the L. acidophilus group, there are some 20 species additional to L. acidophilus sensu stricto (Fig. 3). It is vital at this point to distinguish between the strain- and species-level classifications of constituent isolates within this group. Many of the early research into the L. acidophilus group blurs the lines between bacterial ‘strains’ of the L. acidophilus phylogenetic subgroup (many would now be considered as species that belong to the L. acidophilus group) and the present definition of a bacterial strain, which is deemed to be a subspecies level taxonomic unit (Klein et al., 1998; Kullen et al., 2000).

A lack of rigour and historical understanding of the literature surrounding L. acidophilus taxonomy may have also contributed to confusion in species and strain identification. The reassignment, for example, of a strain once belonging to L. acidophilus (Tuomola & Salminen, 1998) to Lactobacillus johnsonii, as an entirely separate species (Pridmore et al., 2004), had sound systematic support although some later studies have failed to adopt the correct taxonomic nomenclature (Pimentel et al., 2012). The variety of names that may be attributed to a single strain (Table 1), from both culture collections and commercial trademarks, has also potentially led to multiple groups unknowingly working with the same strain referred to by a different name (Yeung et al., 2002). The commercial success of L. acidophilus may have also contributed to the widespread industrial use of what appear to be identical strains because their proprietary protection and use within multiple functional foods or probiotic supplements.

Table 1. Lactobacillus acidophilus strains and their pseudonyms
ATCCaDSMZbBCCM/LMGcNCIMBdOther key namesNotes
  1. a

    American Type Culture Collection, USA.

  2. b

    Deutsche Sammlung von Mikroorganismen und Zellkulturen, Germany.

  3. c

    Belgian Co-ordinated Collections of Microorganisms, Belgium.

  4. d

    National Collection of Industrial, Food and Marine Bacteria, UK.

ATCC 314 LMG 11467   
ATCC 832 LMG 11428NCIMB 1723  
ATCC 4355 LMG 11469   
ATCC 4356TDSM 20079 T

LMG 13550T

LMG 7943 T

LMG 8150 T

LMG 9433 T

NCIMB 701748 T

NCIMB 8690 T

NCFB 1748 T

NCTC 12980 T

Neotype strain (Hansen & Mocquot, 1970)
ATCC 4357DSM 20242LMG 11430NCIMB 8607  
  LMG 13003   
ATCC 4796 LMG 11470  Draft genome sequence (Human Microbiome Project; Turnbaugh et al., 2007)
ATCC 9224 

LMG 11429

LMG 11472

LMG 19170

NCIMB 8116  
ATCC 13651DSM 9126LMG 11466NCIMB 701360  
ATCC 700396   NCFM, N2, NCK56, NCK45, RL8KGenome sequence (Altermann et al., 2005)

Worrying recent examples of incorrect reporting of L. acidophilus include a genome sequence announcement for ‘L. acidophilus’ strain 30SC (Oh et al., 2011). Straightforward bioinformatic characterisation of the 16S rRNA and gyrB genes from the 30SC genome demonstrated the sequence was most likely derived from L. amylovorus (Bull et al., 2012). This misidentification was further corroborated by evolutionary analysis of LAB metabolic pathways which showed those in strain 30SC were also more closely related to L. amylovorus (Salvetti et al., 2013). Another strain that may have been misclassified in the published literature is L. acidophilus LAB20 (Tang et al., 2012; Tang & Saris, 2013). This strain was isolated as a dominant LAB from the gastrointestinal tract of a dog (Tang et al., 2012). Subsequent development of LAB20 strain-specific markers using an S-layer protein gene actually showed this selected marker was phylogenetically more closely related to L. crispatus than a validated L. acidophilus sensu stricto strain (Tang & Saris, 2013). In completing our review, we have collated only publications related to L. acidophilus sensu stricto.

Lactobacillus acidophilus was first isolated in 1900 (Moro) from infant faeces and at the time was designated as Bacillus acidophilus. The multiple strain names of the most commonly encountered L. acidophilus strains are listed in Table 1. The variety of strain names that have been be given to a single isolate deposited in multiple locations further complicates establishing the provenance of a particular strain. The StrainInfo database allows users to visually trace the history of a particular strain and can be used to resolve confusion in many cases (Dawyndt et al., 2005). Fortunately, much of the body of work on L. acidophilus, particularly concerning its probiotic effects, has been undertaken on one particular strain: L. acidophilus NCFM. Although the depth of information available on NCFM has ensured that it is very well characterised as a true strain of L. acidophilus, it still has not escaped the confusion of being known by multiple strain names and may exist in the literature as NCFM, N2, NCK56, NCK45 and RL8K (Table 1). The large body of information concerning L. acidophilus NCFM has contributed to it being deemed generally regarded as safe (GRAS) by the US Food and Drug Administration, as an approved ingredient in dairy products, functional beverages and nutritional powders (Bernardeau et al., 2006).

Basic features of L. acidophilus

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Lactobacillus acidophilus is a short (2–10 μm) Gram-positive rod that grows optimally from 37 to 42 °C (Altermann et al., 2005) and is able to grow at temperatures as high as 45 °C. The species achieves its highest growth rates in slightly acidic media of pH 5.5–6.0, and growth ceases below pH 4.0 (Shah, 2007). It is an obligate homofermenter producing lactic acid from fermentation of carbohydrates and is among the least oxygen tolerant lactobacilli (Archibald & Fridovich, 1981; Claesson et al., 2007).

From examination of the biosynthetic pathways encoded within its genome, L. acidophilus is auxotrophic for 14 amino acids and seems unable to synthesise multiple cofactors and vitamins including riboflavin, vitamin B6, nicotinate, nicotinamide, biotin and folate (Altermann et al., 2005). These deficits in anabolic capacity are exemplified by the need to use nutrient-rich media such as deMan, Rogosa and Sharpe (MRS) agar (de Man et al., 1960; Morishita et al., 1981) for its routine culture. Lactobacillus acidophilus forms at least two colony morphotypes when grown under standard culture conditions on MRS agar, referred to as rough and smooth colonies. The proportion of rough to smooth colony morphotypes exhibited by L. acidophilus is influenced by exposure to antibiotics such as Penicillin G (Khaleghi et al., 2011) or bile (Khaleghi et al., 2010), which both cause a dose-dependent shift towards the smooth morphotype.

Although L. acidophilus has been isolated from multiple human-associated sources, recent phylogenomic characterisation by Claesson et al. (2008) established that the most likely environmental niche of L. acidophilus was the GI tract, with other lactobacilli broadly inhabiting plants and meat. The neotype L. acidophilus strain ATCC 4356 was described as isolated from the human microbiota although the records do not give the precise bodily location from where it was isolated. Metagenomic studies indicate that lactobacilli may compose just 0.2–1% of the total microbiota in the human colon and faeces and also show that their prevalence is highly variable between individuals (Walter, 2008; Kleerebezem & Vaughan, 2009). Lactobacillus acidophilus may be just a small and variable fraction of this low overall carriage of the genus. Culture-independent studies from other hosts also show wide variations in the prevalence of this LAB species. For example, L. acidophilus was present as the most abundant member of the lactobacilli in broiler chickens (Lu et al., 2003), while in contrast, a total absence of L. acidophilus was found in pigs (Leser et al., 2002). Culture-dependent analysis of lactobacilli within the pig GIT suggests they are largely comprised of the L. acidophilus group although no L. acidophilus isolates were specifically recovered (Korhonen et al., 2007). Overall, gut carriage of L. acidophilus appears highly variable.

Human gut passage of L. acidophilus has been modelled in a probiotic capsule feeding study (Mahenthiralingam et al., 2009). Participants were prescreened for faecal presence of L. acidophilus using culture-based methods in tandem with DNA fingerprinting to identify the Lactobacillus strain being administered. Three of the 12 participants were found to be culture positive for L. acidophilus prior to probiotic feeding, indicating faecal carriage of L. acidophilus in humans is not universal (Mahenthiralingam et al., 2009). After feeding (5.6 × 109 viable bacteria per capsule which was taken daily), the administered L. acidophilus strain was detected in 10 of the 12 subjects, reaching cultivatable levels as high as 107 colony-forming units per gram of faeces in three of the volunteers (Mahenthiralingam et al., 2009). Long-term carriage of L. acidophilus for 28 days postfeeding was detected in three subjects, who notably did not culture positive for L. acidophilus before feeding. Overall, these results suggest that dietary intake is a major influence on the human carriage of L. acidophilus.

Food and industrial use of L. acidophilus

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Lactobacillus acidophilus is a major commercial species of the lactic acid bacteria (LAB), available in products including milk, yoghurt and toddler formula, as well as in dietary supplements with reported probiotic effects (Sanders & Klaenhammer, 2001; Altermann et al., 2005). It is part of many undefined starter cultures for milk fermentation, a preservation process developed in the Early Neolithic era and used in the production of traditional fermented foods for more than 10 000 years (Tamime, 2002). Its slow growth in milk (Azcarate-Peril et al., 2009) means that most of the fermentation in milk products is achieved with a yoghurt starter culture (e.g. Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus) and L. acidophilus is subsequently added for additional probiotic value (Shah, 2000).

Probiotic strains of L. acidophilus

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Probiotic bacterial strains are commonly mislabelled or unlabelled in products, often due to the difficulties in discerning both species and strains of Lactobacillus (Yeung et al., 2002). The primary commercial probiotic strains of L. acidophilus are described by Shah (2007) and include L. acidophilus LA-1 and LA-5 (Chr. Hansen, Denmark), NCFM (Dansico, Madison), DDS-1 (Nebraska Cultures, Nebraska) and SBT-2026 (Snow Brand Milk Products, Tokyo, Japan). Lactobacillus acidophilus NCFM, a major commercial strain, has identical fermentation and growth characteristics to the Type strain ATCC 4356T and is also closely related to PFGE profile (Sanders & Klaenhammer, 2001). Lactobacillus acidophilus isolated from products claimed to contain strain LA-5 also produce DNA fingerprints with a high degree of similarity (91.9%) to the L. acidophilus ATCC 4356T by randomly amplified polymorphic DNA (RAPD) fingerprint analysis (Schillinger et al., 2003). Lactobacillus acidophilus LA-1 is no longer available as a product from Chr. Hansen. A wealth of research dedicated to ‘L. acidophilus La1’ a commercial strain marketed by Nestlé may also be found in the published literature (Link-Amster et al., 1994). However, this strain has subsequently been taxonomically reassigned to L. johnsonii and has a genome sequence available as L. johnsonii NCC 533 (Pridmore et al., 2004). Comparative information on the differences in probiotic effect between each commercial strain is not available, however, it is recognised that different Lactobacillus species may display similar probiotic effects in vitro, yet have markedly divergent properties when assessed in vivo (Ibnou-Zekri et al., 2003).

Probiotic characteristics and physiology

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

The probiotic effects of L. acidophilus NCFM are well characterised, aided recently by the availability of its genome sequence and the necessity of in-depth characterisation for application for GRAS status. Although a genome sequence is not (yet) available, L. acidophilus LA-5 is similarly characterised for patent claim information. The characterisation of probiotic strains may be broadly divided into two categories. The first is desirable probiotic physiology demonstrable in vitro such as stability in products (Shah, 2000), resistance to bile (Pfeiler et al., 2007; Pfeiler & Klaenhammer, 2009; Khaleghi et al., 2010) and tolerance to low pH (Azcarate-Peril et al., 2004, 2005), adherence to human colonocytes in cell culture (Buck et al., 2005), antimicrobial production (Sanders & Klaenhammer, 2001; Tabasco et al., 2009) and lactase activity (Sanders et al., 1996). The second category encompasses the gross probiotic effect observable in the context of feeding studies such as mediation of host immune response (Bron et al., 2012), lowering host serum cholesterol (Shah, 2007), improving host lactose metabolism (Gilliland, 1989) and preventing or treating infection (Wang et al., 2004). Several recent clinical trials have also shown that consumption of probiotics containing L. acidophilus NCFM in combination with Bifidobacterium species can produce health benefits, the ‘gold standard’ for a probiotic claim. For example, they reduce bloating in adults with functional bowel disorders (Ringel-Kulka et al., 2011) and suppress cold and influenza-like symptoms in children (Leyer et al., 2009).

Analysis of the L. acidophilus NCFM genome sequence has directly facilitated the functional characterisation of its ability to tolerate exposure to both low pH and bile, important factors for a probiotic organism that must pass through the gastrointestinal tract. Functional microarray experiments with L. acidophilus NCFM showed upregulation of transcripts from three transporter genes [two major facilitator (MFC) superfamily and the permease component of an ABC transporter] in the presence of bile (Pfeiler et al., 2007). Similar transporters had previously been shown in other species to be involved in bile efflux from the cell (Solheim et al., 2007). Furthermore, a study that generated deletion mutants lacking these three transporter genes showed a significant decrease in their ability to survive in bile (Pfeiler & Klaenhammer, 2009). Lactobacillus acidophilus NCFM is also able to survive exposure to pH 3.0 for 5 h with no loss of viability (Azcarate-Peril et al., 2004).

Lactobacillus acidophilus is able to utilise a variety of carbon sources for growth (Sanders & Klaenhammer, 2001; Yeung et al., 2004), but a comprehensive understanding of the mechanisms behind the uptake and metabolism of carbon sources has not yet been achieved. A study describing several genetic loci responsible for carbohydrate metabolism again demonstrated the utility of the L. acidophilus complete genome sequence (Barrangou et al., 2006). Several classes of transporter (ATP-binding cassette, phosphoenol-pyruvate phosphotransferase system and galactoside pentose hexuronide permease) were found to be induced in the presence of their respective substrates but repressed in the presence glucose, suggesting that carbohydrate metabolism in L. acidophilus is strongly regulated by catabolite repression. The strong link between carbohydrate source and regulation of sugar uptake and metabolism genes likely contributes to the competitive ability of L. acidophilus in the human gastrointestinal tract. The metabolism of these complex carbohydrates also provides a function that is not present in humans and other microbiota, potentially enriching the growth of L. acidophilus and other probiotic LAB in the human gastrointestinal tract (Zhu et al., 2009). Studies have demonstrated the ability of L. acidophilus to adhere to human Caco-2 colonocytes in vitro. An analysis of the adhesion factors involved in L. acidophilus NCFM-Caco-2 epithelial cell interaction found significant involvement in S-layer proteins, linked to the gene slpA, fibronectin-binding protein (FbpA) and mucin-binding protein (Mub; Buck et al., 2005).

Genomic features

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

The genome sequence of L. acidophilus NCFM was the third of the Lactobacillus genomes to be published, behind Lactobacillus plantarum WCFS1 (Kleerebezem et al., 2003) and L. johnsonii NCC 533 (Pridmore et al., 2004), and the first genome sequence from an L. acidophilus phylogenetic subgroup species (Table 2). In silico analyses of the L. acidophilus NCFM genome shows it is able to synthesise a limited number of amino acids (cysteine, serine and aspartate) and to compensate it's genome is enriched in genes coding for amino acid transport and fermentative functions (Altermann et al., 2005). The comparatively small (1 993 564 bp) genome of L. acidophilus has a low (35%) average GC content, compared with other members of the L. acidophilus phylogenetic subgroup (mean GC content = 40%), which have an upper range of 50% GC (L. delbrueckii subsp. bulgaricus). The GC content of the L. acidophilus genome is inherently higher (up to 50%) in the four regions containing rRNA genes as expected (Altermann et al., 2005). Other than GC content, basic genomic attributes such as size and gene content do not vary significantly from other member of the L. acidophilus group.

Table 2. Completed and published genome sequences from the Lactobacillus acidophilus group
OrganismStrainOrigin/UseGC (mol %)Genome size (Mb)Gene countCRISPR countCoding base count%PlasmidsPublication
Lactobacillus acidophilus NCFMProbiotic351.991970189.640Altermann et al. (2005)
Lactobacillus amylovorus GRL 1118Pig intestine381.981994386.862 Kant et al. (2011a)
Lactobacillus amylovorus GRL 1112Pig intestine382.132193086.992 Kant et al. (2011b)
Lactobacillus crispatus ST1Chicken372.042100389.370Ojala et al. (2010)
Lactobacillus delbrueckii subsp. bulgaricusATCC 11842Yoghurt501.862234176.010van de Guchte et al. (2006)
Lactobacillus delbrueckii subsp. bulgaricusATCC BAA-365Cheese, yoghurt501.861865179.630Makarova et al. (2006)
Lactobacillus delbrueckii subsp. bulgaricus2038Milk, Probiotic501.871907184.520Hao et al. (2011)
Lactobacillus delbrueckii subsp. bulgaricusND02Milk, Probiotic502.132139284.821Sun et al. (2011)
Lactobacillus gasseri ATCC 33323Human, probiotic351.891874090.110Makarova et al. (2006)
Lactobacillus helveticus DPC 4571Cheese372.081830174.80Callanan et al. (2008)
Lactobacillus helveticus R0052Probiotic372.132084080.221Tompkins et al. (2012)
Lactobacillus helveticus H10Fermented milk372.172052281.321Zhao et al. (2011)
Lactobacillus johnsonii DPC 6026Human351.971840288.60Guinane et al. (2011)
Lactobacillus johnsonii FI9785Human341.791804089.642Wegmann et al. (2009)
Lactobacillus johnsonii NCC 533Probiotic351.991941091.090Pridmore et al. (2004)
Lactobacillus kefiranofaciens ZW3Kefir, Probiotic372.352222380.762Wang et al. (2011)

Plasmids are also common features of members of the L. acidophilus group, present in seven of the 16 strains detailed in Table 2. Their distribution is heterogeneous, with multiple strains of some species with the same number of plasmids (L. amylovorus), some species showing strains with and without plasmids (L. johnsonii and L. helveticus) and others showing no evidence of plasmids at all (L. acidophilus and L. gasseri). Despite the lack of L. acidophilus NCFM and L. johnsonii NCC 533 plasmids, a recent study examining phylogenetic trees of 401 proteins identified horizontal gene transfer (HGT) of up to 40% of the core genome genes between the two species, causing an unprecedented level of phylogenetic incongruence (Nicolas et al., 2007).

One genomic feature that does vary considerably across Lactobacillus genomes is clustered regularly spaced short palindromic repeat (CRISPR) regions. CRISPRs are commonly identified in Lactobacillus genomes from the L. acidophilus phylogenetic subgroup (Table 2) and beyond, with approximately half (26/53) of the sequenced Lactobacillus genomes possessing CRISPR regions, as identified by BlastP (Koonin & Makarova, 2009). The L. acidophilus NCFM CRISPR region has features characteristic of these regions, being c. 1.5 kb in size and composed of 32 near-perfect 29 base repeats, interspersed with unique 32 base spacer DNAs (Altermann et al., 2005). No physiological function was attributed to CRISPR regions at the time of the NCFM genome publication (Altermann et al., 2005), however, subsequent observations that the unique CRISPR spacer sequences were almost identical to fragments of virus and plasmid genes led to the hypothesis that CRISPR regions may be involved in defence against selfish DNA elements (Makarova et al., 2011). This hypothesis has been validated by the demonstration that a short phage-like sequence inserted into the CRISPR locus of Streptococcus thermophilus conferred resistance against its cognate phage (Barrangou et al., 2007).

Prophages and phage interactions are commonly encountered in both the study of LAB genomics and the large-scale manufacture of fermented products by LAB (Mahony et al., 2012), where as a result of the economic implications of phage contamination in dairy fermentations, many LAB phages have been well characterised (Brüssow, 2001). The genome sequence of L. acidophilus NCFM revealed evidence of three isolated phage remnants, or potential autonomous units (PAUs) designated PauLA-I-III. Each PAU is composed of seven core ORFs, with synteny and ORF size highly conserved between PauLA-I and PauLA-II, with PauLA-III lacking a single ORF of hypothetical function. The high degree of similarity between PauLA-I and PauLA-II suggests that these may have been formed following a duplication event, and PauLA-III was evolved in a different organism and was integrated at a different time to the progenitor or PauLA-I and PauLA-II (Altermann et al., 2005). Interestingly, there is an absence of literature on functional bacteriophages capable of infecting strains of L. acidophilus sensu stricto compared with other members of L. acidophilus phylogenetic subgroup.

Conclusions and perspective

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

Lactobacillus acidophilus is an important commercial bacterium with a long history that plays a pivotal role in the characterisation of the genus Lactobacillus. However, given the highly progressive nature of Lactobacillus taxonomy, L. acidophilus as a species has struggled with being misidentified and misrepresented in its past characterisation. Given the increased regulatory criteria being placed on the definition and sale of microbial species as probiotics, L. acidophilus strain NCFM has emerged as one of the most well-characterised probiotics within this species. However, for other areas of study such as the investigation of environmental niches or microbial composition of fermented foods, care should be taken to clearly identify whether L. acidophilus sensu stricto strains are present. Going forward, it will be important to clarify data provided for both (i) the species level Lactobacillus identification, by ensuring new publications are not made with references to old taxonomic names and (ii) the strain level identification of L. acidophilus, by conducting comparisons to well-characterised control strains. Ensuring that these parameters are clearly defined for L. acidophilus will overcome problems with the multiple strain names used for the same original ‘isolate’ greatly improve our understanding of this biotechnologically important Lactobacillus species.

Acknowledgements

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References

M.B. acknowledges funding from the Biotechnology and Biological Sciences Research Council PhD funding with CASE sponsorship from Cultech Ltd., Baglan, Wales, UK. SP is a member of the board of directors at Cultech Ltd. and declares a conflict of interest in relation to co-sponsorship of these research studies.

References

  1. Top of page
  2. Abstract
  3. Introduction
  4. Taxonomy of the lactobacilli
  5. Lactobacillus acidophilus strains and their history
  6. Basic features of L. acidophilus
  7. Food and industrial use of L. acidophilus
  8. Probiotic strains of L. acidophilus
  9. Probiotic characteristics and physiology
  10. Genomic features
  11. Conclusions and perspective
  12. Acknowledgements
  13. References