Assessment of the bacterial diversity of human colostrum and screening of staphylococcal and enterococcal populations for potential virulence factors

Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data

The impaired mucociliary clearance in individuals with Cystic Fibrosis (CF) enables opportunistic pathogens to colonize CF lungs. Here we show that Rothia mucilaginosa is a common CF opportunist that was present in 83% of our patient cohort, almost as prevalent as Pseudomonas aeruginosa (89%). Sequencing of lung microbial metagenomes identified unique R. mucilaginosa strains in each patient, presumably due to evolution within the lung. The de novo assembly of a near-complete R. mucilaginosa (CF1E) genome illuminated a number of potential physiological adaptations to the CF lung, including antibiotic resistance, utilization of extracellular lactate, and modification of the type I restriction-modification system. Metabolic characteristics predicted from the metagenomes suggested R. mucilaginosa have adapted to live within the microaerophilic surface of the mucus layer in CF lungs. The results also highlight the remarkable evolutionary and ecological similarities of many CF pathogens; further examination of these similarities has the potential to guide patient care and treatment.

Bacteriological, biochemical, and immunological modifications in human colostrum after Holder pasteurisation

OBJECTIVE

The objective of this work was to evaluate the effect of Holder pasteurisation of human colostrum on a variety of microbiological, biochemical, and immunological parameters.

METHODS

Colostrum samples from 10 donors, and 8 samples of mature milk used as controls, were heated at 62.5°C for 30 minutes. Bacterial counts and the concentration of furosine, lactose, myoinositol, glucose, lactulose, cytokines, and immunoglobulins were determined before and after the heat treatment.

RESULTS

Mean bacterial counts in nonpasteurised colostrum samples oscillated between 2.72 and 4.13 log10 colony-forming units per millilitre in the agar media tested. Holder pasteurisation led to the destruction of the bacteria originally present in the samples. Furosine was detected in all samples before pasteurisation and increased significantly after the heat treatment (from 6.60 to 20.59 mg/100 g protein). Lactulose content was below the detection limit in nonpasteurised colostrum, but it was detected in all samples and quantified in 7 of them (from 10.68 to 38.02 mg/L) after Holder pasteurisation. Lactose, glucose, and myoinositol concentrations did not change after Holder pasteurisation. The concentrations of most cytokines and immunoglobulins were significantly higher in colostrum than in mature milk samples. Immunoglobulin content, both in colostrum and in milk samples, was reduced during pasteurisation, whereas, among cytokines, only macrophage inflammatory protein-1β, interleukin-7, and granulocyte-macrophage-colony-stimulating factor concentrations were affected by this heat treatment.

CONCLUSIONS

Lactulose and furosine content could be used as heat treatment indicators in colostrum samples. Holder pasteurisation modified the immunological profile of both colostrum and mature milk.

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

BACKGROUND

Necrotizing enterocolitis (NEC) is a devastating intestinal disease that afflicts 10% of extremely preterm infants. The contribution of early intestinal colonization to NEC onset is not understood, and predictive biomarkers to guide prevention are lacking. We analyzed banked stool and urine samples collected prior to disease onset from infants <29 weeks gestational age, including 11 infants who developed NEC and 21 matched controls who survived free of NEC. Stool bacterial communities were profiled by 16S rRNA gene sequencing. Urinary metabolomic profiles were assessed by NMR.

RESULTS

During postnatal days 4 to 9, samples from infants who later developed NEC tended towards lower alpha diversity (Chao1 index, P = 0.086) and lacked Propionibacterium (P = 0.009) compared to controls. Furthermore, NEC was preceded by distinct forms of dysbiosis. During days 4 to 9, samples from four NEC cases were dominated by members of the Firmicutes (median relative abundance >99% versus <17% in the remaining NEC and controls, P < 0.001). During postnatal days 10 to 16, samples from the remaining NEC cases were dominated by Proteobacteria, specifically Enterobacteriaceae (median relative abundance >99% versus 38% in the other NEC cases and 84% in controls, P = 0.01). NEC preceded by Firmicutes dysbiosis occurred earlier (onset, days 7 to 21) than NEC preceded by Proteobacteria dysbiosis (onset, days 19 to 39). All NEC cases lacked Propionibacterium and were preceded by either Firmicutes (≥98% relative abundance, days 4 to 9) or Proteobacteria (≥90% relative abundance, days 10 to 16) dysbiosis, while only 25% of controls had this phenotype (predictive value 88%, P = 0.001). Analysis of days 4 to 9 urine samples found no metabolites associated with all NEC cases, but alanine was positively associated with NEC cases that were preceded by Firmicutes dysbiosis (P < 0.001) and histidine was inversely associated with NEC cases preceded by Proteobacteria dysbiosis (P = 0.013). A high urinary alanine:histidine ratio was associated with microbial characteristics (P < 0.001) and provided good prediction of overall NEC (predictive value 78%, P = 0.007).

CONCLUSIONS

Early dysbiosis is strongly involved in the pathobiology of NEC. These striking findings require validation in larger studies but indicate that early microbial and metabolomic signatures may provide highly predictive biomarkers of NEC.

Genetic relatedness of coagulase-negative Staphylococci from gastrointestinal tract and blood of preterm neonates with late-onset sepsis

BACKGROUND

Coagulase-negative staphylococci (CoNS) are the first colonizers of gastrointestinal tract (GIT) and the commonest cause of late-onset sepsis (LOS) in preterm neonates. Intravascular catheters are considered a major source of CoNS bacteremia. However, several cases of LOS remain without an identified source. To elucidate whether GIT could be a potential source of invasive strains, we aimed to assess the molecular similarity between CoNS from blood and GIT in preterm neonates with LOS.

METHODS

Altogether 22 blood and 53 GIT isolates collected from 22 neonates with LOS caused by CoNS (Staphylococcus haemolyticus in 13, Staphylococcus epidermidis in 7 and Staphylococcus hominis in 2 patients) were included. Rectal swabs were collected twice weekly from birth, but only isolates obtained before LOS were analyzed. S. epidermidis isolates were typed by multilocus variable number of tandem repeats analysis and multilocus sequence typing, S. haemolyticus by pulsed-field gel electrophoresis.

RESULTS

Eighteen of 22 neonates had the same CoNS species in GIT and bloodstream; all these isolates from them (altogether 18 blood and 28 GIT isolates) underwent typing. The genotypic similarity between bloodstream and ≥1 antecedent GIT isolates was observed in 13 of 18 patients-3 of 7 with S. epidermidis and 10 of 11 with S. haemolyticus infection. The concordant GIT isolates were collected 0-7 days before the positive blood culture.

CONCLUSIONS

The similarity between CoNS from GIT and bloodstream indicates that preterm neonates harbour invasive strains in GIT before LOS. Whether there is a causal relationship between GIT colonization and LOS remains to be elucidated in further studies.

Human milk: a source of more life than we imagine

The presence of bacteria in human milk has been acknowledged since the seventies. For a long time, microbiological analysis of human milk was only performed in case of infections and therefore the presence of non-pathogenic bacteria was yet unknown. During the last decades, the use of more sophisticated culture-dependent and -independent techniques, and the steady development of the -omic approaches are opening up the new concept of the ‘milk microbiome’, a complex ecosystem with a greater diversity than previously anticipated. In this review, possible mechanisms by which bacteria can reach the mammary gland (contamination versus active migration) are discussed. In addition, the potential roles of human milk for both infant and maternal health are summarised. A better understanding of the link between the milk microbiome and health benefit, the potential factors influencing this relationship and whether or not it can be influenced by nutrition is required to open new avenues in the field of pregnancy and lactation.

Complete genome sequence of Streptococcus salivarius PS4, a strain isolated from human milk

Streptococcus salivarius is a commensal species commonly found in the human oropharyngeal tract. Some strains of this species have been developed for use as oral probiotics, while others have been associated with a variety of opportunistic human infections. Here, we report the complete sequence of strain PS4, which was isolated from breast milk of a healthy woman.

Microbial contact during pregnancy, intestinal colonization and human disease

Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host-microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host-microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host-microbe interaction to reduce the risk of disease in the child.

The human milk microbiota: origin and potential roles in health and disease

Human milk has been traditionally considered sterile; however, recent studies have shown that it represents a continuous supply of commensal, mutualistic and/or potentially probiotic bacteria to the infant gut. Culture-dependent and -independent techniques have revealed the dominance of staphylococci, streptococci, lactic acid bacteria and bifidobacteria in this biological fluid, and their role on the colonization of the infant gut. These bacteria could protect the infant against infections and contribute to the maturation of the immune system, among other functions. Different studies suggest that some bacteria present in the maternal gut could reach the mammary gland during late pregnancy and lactation through a mechanism involving gut monocytes. Thus, modulation of maternal gut microbiota during pregnancy and lactation could have a direct effect on infant health. On the other hand, mammary dysbiosis may lead to mastitis, a condition that represents the first medical cause for undesired weaning. Selected strains isolated from breast milk can be good candidates for use as probiotics. In this review, their potential uses for the treatment of mastitis and to inhibit mother-to-infant transfer of HIV are discussed.

Cultures of Holder-pasteurized donor human milk after use in a neonatal intensive care unit

OBJECTIVE

Current guidelines state that human milk, once thawed, should be kept in a refrigerator for only 24 hours. We cultured Holder-pasteurized donor human milk (DHM) after thawing and refrigeration under clinical conditions.

STUDY DESIGN

Bottles of pasteurized DHM were thawed and used in a regional level 3 neonatal intensive care unit (NICU) in standard clinical fashion and kept refrigerated when not in use. Once no longer needed clinically, aliquots were cultured for bacteria.

RESULTS

In total, 30 bottles were returned for culture; six were excluded from analysis because human milk fortifier had been added, and two had been left out of the refrigerator. The remaining 22 bottles were culture-negative after having been thawed for 7-122 hours.

CONCLUSIONS

DHM without additives was culture-negative for 24 hours or longer after thawing and routine NICU handling. These data indicate that unfortified Holder-pasteurized DHM handled appropriately and refrigerated remains sterile for 24 hours after thawing and perhaps longer. Further study is needed to confirm this.

Bacterial biofilms associated with food particles in the human large bowel

Bacteria within the gastro-intestinal tract affect host function via production of short-chain fatty acids and synthesis of vitamins. Additionally, the commensal enteric bacteria modulate the immune system and provide protection from potentially pathogenic bacteria. Only recently heterogeneous bacterial biofilms were found to be associated with food particles within the intestinal tract. There are a number of studies investigating the formation and function of pathogenic and single-species biofilms, though few studies have investigated the dynamics of multispecies biofilms, especially with regard to food/microbial/host interactions. The scope of this review is to discuss the current knowledge of bacterial biofilms associated with food particles in the human large bowel, examine the established mathematical models depicting bacterial attachment, and elucidate key areas for further research.

Streptococcus lactarius sp. nov., isolated from breast milk of healthy women

Three strains of a hitherto-unknown, Gram-stain-positive coccus were recovered from the milk of three non-related healthy women. The isolates shared 99 % 16S rRNA gene sequence similarity with sequences from uncultured members of the Lactobacillales and Streptococcus. The closest sequence corresponding to a defined species was that of Streptococcus peroris GTC 848T, with a similarity of 98 %. A partial sequence (488 bp) of the tuf gene also showed 97 % similarity with that of S. peroris CCUG 39814T. The combined 16S rRNA/tuf-based phylogeny revealed that all the isolates grouped in a statistically well-supported cluster separate from S. peroris. Enzyme activity profiles as well as fermentation patterns differentiated the novel bacteria from other members of the Streptococcus mitis group. Finally, phenotypic, genotypic and phylogenetic data supported the proposal of a novel species of the genus Streptococcus, for which the name Streptococcus lactarius sp. nov. is proposed. The type strain is MV1T ( = CECT 7613T  = DSM 23027T).

Inhibition of human immunodeficiency virus type 1 by lactic acid bacteria from human breastmilk

BACKGROUND

Human breastmilk provides a rich source of commensal lactic acid bacteria (LAB) to the infant during breastfeeding and stimulates abundant growth and colonization of these bacteria at mucosal surfaces in the infant gastrointestinal tract. While conferring critical nutritional and immunologic support to the developing newborn, breastmilk also serves as a vehicle for human immunodeficiency virus type 1 (HIV-1) transmission from mother to child during breastfeeding. Whether breastmilk LAB confer protection against mucosal exposure to HIV-1 in breastfeeding infants is unknown.

STUDY DESIGN

In the present study, we sought to evaluate LAB isolated from the breastmilk of healthy women for the ability to inhibit HIV-1 infection in vitro. A total of 38 strains of breastmilk bacteria were evaluated in this study. Both heat-killed bacteria and cell-free conditioned supernatants from bacterial cultures were tested for the ability to inhibit infection with HIV-1 using viral isolates with tropism for CCR5 (R5), CXCR4 (X4), or R5/X4 dual-tropism.

RESULTS

Significant inhibition of R5-tropic HIV-1 was demonstrated using heat-killed bacteria, most notably among breastmilk strains of Lactobacillus and Pediococcus. Selected strains of breastmilk LAB also demonstrated significant inhibition of HIV-1 infection against virus with tropism for X4 and R5/X4.

CONCLUSION

These results demonstrate for the first time that commensal LAB from human breastmilk inhibit HIV-1 infection in vitro and suggest a possible role for these bacteria in mucosal protection against HIV-1 in the breastfeeding infant.

Complete genome sequence of Lactobacillus salivarius CECT 5713, a probiotic strain isolated from human milk and infant feces

Lactobacillus salivarius is a homofermentative lactic acid bacterium and is frequently isolated from mucosal surfaces of healthy humans. L. salivarius CECT 5713, a strain isolated simultaneously from breast milk and infant feces of a healthy mother-infant pair, has immunomodulatory, anti-inflammatory, and anti-infectious properties, as revealed by several in vitro and in vivo assays. Here, we report its complete and annotated genome sequence.

Enterocin C, a class IIb bacteriocin produced by E. faecalis C901, a strain isolated from human colostrum

Enterocin C (EntC), a class IIb bacteriocin was purified from culture supernatants of Enterococcus faecalis C901, a strain isolated from human colostrum. Enterocin C consists of two distinct peptides, named EntC1 and EntC2, whose complementary action is required for full antimicrobial activity. The structural genes entC1 and entC2 encoding enterocins EntC1 and EntC2, respectively, and that encoding the putative immunity protein (EntCI) are located in the 9-kb plasmid pEntC, harboured by E. faecalis C901. The N-terminal sequence of both antimicrobial peptides revealed that EntC1 (4284 Da) is identical to Ent1071A, one of the two peptides that form enterocin 1071 (Ent1071), a bacteriocin produced by E. faecalis BFE 1071. In contrast, EntC2 (3867 Da) presents the non-polar alanine residue at position 17 (Ala(17)) instead of the polar threonine residue (Thr(17)) in Ent1071B, the second peptide constituting Ent1071. In spite of peptide similarities, EntC differs from Ent1071 in major aspects, including the complementary activity among its constitutive peptides and its wider inhibitory spectrum of activity. Different amphiphilic alpha-helical conformations between EntC2 and Ent1071B could explain both, acquired complementary activity and increased antimicrobial spectrum.

Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR

AIMS

Breast milk has been described as a source of bacteria influencing the development of the infant gut microbiota. Up to the present, few studies have been focused on the application of culture-independent techniques to study bacterial diversity in breast milk. In this context, the aim of this study was to characterize the breast milk microbiota of healthy women by applying the quantitative real-time PCR technique (qRTi-PCR).

METHODS AND RESULTS

A total of 50 breast milk samples were analysed by qPCR to assess the presence of different bacterial genera or clusters, including the Bifidobacterium, Lactobacillus, Staphylococcus, Bacteroides, Enterococcus, Streptococcus, Clostridium cluster IV and Clostridium cluster XIVa-XIVb groups. Staphylococcus, Streptococcus, Bifidobacterium and Lactobacillus were the predominant groups and were detected in all the samples. Clostridium XIVa-XIVb and Enterococcus were detected in most of the samples in contrast to the Bacteroides and Clostridium cluster IV groups.

CONCLUSIONS

Our results confirm the abundance of bacterial DNA in breast milk samples and suggest that the qRTi-PCR technique has a huge potential in the microbiological analysis of human milk.

SIGNIFICANCE AND IMPACT OF THE STUDY

qRTi-PCR allowed the detection of bacterial DNA of streptococci, staphylococci, lactic acid bacteria and bifidobacteria in the samples of human milk, which confirms that breast milk can be an important source of bacteria and bacterial DNA to the infant gut.