Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

ABSTRACT The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function. Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32). Fecal samples were collected during the first 60 postnatal days in both groups. Fecal samples were assessed by 16S rRNA gene sequencing, quantitative PCR, mass spectrometry, and endotoxin measurement. B. infantis-fed infants had significantly higher populations of fecal Bifidobacteriaceae, in particular B. infantis, while EVC001 was fed, and this difference persisted more than 30 days after EVC001 supplementation ceased. Fecal milk oligosaccharides were significantly lower in B. infantis EVC001-fed infants, demonstrating higher consumption of human milk oligosaccharides by B. infantis EVC001. Concentrations of acetate and lactate were significantly higher and fecal pH was significantly lower in infants fed EVC001, demonstrating alterations in intestinal fermentation. Infants colonized by Bifidobacteriaceae at high levels had 4-fold-lower fecal endotoxin levels, consistent with observed lower levels of Gram-negative Proteobacteria and Bacteroidetes. IMPORTANCE The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function.

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Taxonomic signatures of cause-specific mortality risk in human gut microbiome

Nature Communications ◽

10.1038/s41467-021-22962-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Aaro Salosensaari ◽

Ville Laitinen ◽

Aki S. Havulinna ◽

Guillaume Meric ◽

Susan Cheng ◽

...

Keyword(s):

Mortality Risk ◽

Gut Microbiome ◽

Human Gut ◽

Cross Sectional ◽

Microbiome Composition ◽

Human Gut Microbiome ◽

Non Invasive ◽

Sequencing Technologies

AbstractThe collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

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Distinct dietary alpha-linolenic acid-dependent shifts in the fecal microbiome composition suppresses aging-associated inflammatory responses and thrombus formation

European Heart Journal ◽

10.1093/ehjci/ehaa946.3773 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

S.S Saeedi Saravi ◽

N.R Bonetti ◽

G.G Camici ◽

T.F Luscher ◽

J.H Beer

Keyword(s):

Platelet Aggregation ◽

Shear Flow ◽

Plasma Levels ◽

Inflammatory Responses ◽

Thrombus Formation ◽

Funding Source ◽

High Shear ◽

Fecal Microbiome ◽

Microbiome Composition

Abstract Background Aging is associated with alterations in the fecal microbiome composition. The microbiota-derived trimethylamine-N-oxide (TMAO) correlates with arterial thrombotic events, e.g. myocardial infarction and stroke, the leading causes of mortality worldwide. The omega-3 fatty acid (n-3 FA) α-linolenic acid (ALA) has been shown to be protective against thrombosis and associated pathologies. Therefore, we hypothesized that long-term dietary ALA supplementation protects against the aging-associated microbiome dysbiosis, and reduces inflammatory and thrombotic responses. Methods 24 week-old male C57BL/6 mice were fed either a high ALA (7.3g%) or low ALA (0.03g%) diet for 12 months. We examined the compositional changes of fecal microbiota of the animals treated with high vs. low ALA via 16S rRNA gene sequencing. The plasma levels of TMAO and its precursors choline and betaine, and LPS were measured by ELISA. Additionally, the platelet aggregation in response to thrombin, and thrombus formation on collagen under high-shear flow conditions of 3000/sec (to mimic blood flow in stenosed arteries) were investigated. Results Genomic analyses showed that the abundance of Phylum Proteobacteria and the family of desulfovibrio were reduced 71.72% and 51.73% in the aged high ALA-treated mice (p<0.01 and p<0.001, resp.) that may result in decrease in TAMO production and the subsequent inflammatory responses. However, microbial diversity of Bacteroidetes or Fermicutes and Bacteroidetes/Fermicutes ratio did not demonstrate a significant change between high vs. low ALA groups. Interestingly, the dietary intake of high ALA increased the abundance of Lachnospiraceae (p<0.01) that may exert anti-inflammatory effects. Importantly, high ALA significantly decreased the plasma levels of TMAO (p<0.01) and its precursor choline (P<0.05), but not betaine. The pro-inflammatory cytokine TNF-α showed a significant reduction (p<0.05), whereas plasma IL-1β did not change significantly following high ALA supplementation. An increased thrombus formation on collagen under high-shear flow (36.34%, p<0.01) and thrombin-induced platelet aggregation (31.31%, p<0.05) were found in the aged mice. Conclusion These studies demonstrate that an ALA-rich diet induces beneficial bacterial shifts in the aging-associated fecal microbiome that may lead to the suppression of inflammatory and thrombotic responses. Hence, long-term dietary ALA supplementation may be exploited as a nutritional antithrombotic strategy in the aging. Microbiome-Thrombosis-Aging Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): Swiss National Science Foundation (SNSF)

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Basal Diet Determined Long-Term Composition of the Gut Microbiome and Mouse Phenotype to a Greater Extent than Fecal Microbiome Transfer from Lean or Obese Human Donors

Nutrients ◽

10.3390/nu11071630 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1630 ◽

Cited By ~ 6

Author(s):

Daphne M. Rodriguez ◽

Abby D. Benninghoff ◽

Niklas D.J. Aardema ◽

Sumira Phatak ◽

Korry J. Hintze

Keyword(s):

Gut Microbiome ◽

Basal Diet ◽

Body Type ◽

Human Donor ◽

Final Body Weight ◽

Linear Discriminant ◽

Fecal Microbiome ◽

Microbiome Composition ◽

Diet Induced Obesity ◽

Obese Human

The Western dietary pattern can alter the gut microbiome and cause obesity and metabolic disorders. To examine the interactions between diet, the microbiome, and obesity, we transplanted gut microbiota from lean or obese human donors into mice fed one of three diets for 22 weeks: (1) a control AIN93G diet; (2) the total Western diet (TWD), which mimics the American diet; or (3) a 45% high-fat diet-induced obesity (DIO) diet. We hypothesized that a fecal microbiome transfer (FMT) from obese donors would lead to an obese phenotype and aberrant glucose metabolism in recipient mice that would be exacerbated by consumption of the TWD or DIO diets. Prior to the FMT, the native microbiome was depleted using an established broad-spectrum antibiotic protocol. Interestingly, the human donor body type microbiome did not significantly affect final body weight or body composition in mice fed any of the experimental diets. Beta diversity analysis and linear discriminant analysis with effect size (LEfSe) showed that mice that received an FMT from obese donors had a significantly different microbiome compared to mice that received an FMT from lean donors. However, after 22 weeks, diet influenced the microbiome composition irrespective of donor body type, suggesting that diet is a key variable in the shaping of the gut microbiome after FMT.

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Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother–Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses

Frontiers in Nutrition ◽

10.3389/fnut.2021.813690 ◽

2022 ◽

Vol 8 ◽

Author(s):

Yosuke Komatsu ◽

Daiki Kumakura ◽

Namiko Seto ◽

Hirohisa Izumi ◽

Yasuhiro Takeda ◽

...

Keyword(s):

Breast Milk ◽

Gut Microbiome ◽

Lactation Period ◽

Bioactive Components ◽

Fecal Microbiome ◽

Breastfed Infants ◽

H Nmr ◽

Milk Components ◽

Infant Gut Microbiome ◽

Infant Feces

Background: The gut microbiome and fecal metabolites of breastfed infants changes during lactation, and are influenced by breast milk components. This study aimed to investigate dynamic associations of milk components with the infant gut microbiome and fecal metabolites throughout the lactation period in a mother–infant model.Methods: One month after delivery, breast milk and subsequent infant feces were collected in a pair for 5 months from a mother and an exclusively breastfed infant. Composition of the fecal microbiome was determined with 16S rRNA sequencing. Low-molecular-weight metabolites, including human milk oligosaccharides (HMOs), and antibacterial proteins were measured in feces and milk using 1H NMR metabolomics and enzyme-linked immunosorbent assays. The association of milk bioactive components with the infant gut microbiome and fecal metabolites was determined with Python clustering and correlation analyses.Results: The HMOs in milk did not fluctuate throughout the lactation period. However, they began to disappear in infant feces at the beginning of month 4. Notably, at this time-point, a bifidobacterium species switching (from B. breve to B. longum subsp. infantis) occurred, accompanied by fluctuations in several metabolites including acetate and butyrate in infant feces.Conclusions: Milk bioactive components, such as HMOs, might play different roles in the exclusively breastfed infants depending on the lactation period.

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Maximizing Nutrient Availability for the Breastfed Infant Through Colonization with B. Infantis EVC001 (FS04-04-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz048.fs04-04-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Tracy Shafizadeh ◽

Steve Frese ◽

Giorgio Casaburi

Keyword(s):

Human Milk ◽

Nutrient Availability ◽

Gut Microbiome ◽

Bifidobacterium Longum ◽

Developed Countries ◽

Breastfed Infant ◽

Control Group ◽

Term Infants ◽

Fecal Samples ◽

Infant Gut Microbiome

Abstract Objectives Human breastmilk contains complete nutrient composition required for the developing infant, including human milk oligosaccharides (HMO). These complex carbohydrates are indigestible by the infant alone, and require digestion by gut microbes, namely Bifidobacterium longum subsp. infantis (B. infantis). However, decades of C-section delivery, formula feeding and increasing exposure to antibiotics have contributed the loss of this critical infant-associated gut bacterium in developed countries. Therefore, restoring B. infantis to the infant gut was hypothesized to improve the nutritional utilization of human breastmilk in healthy term infants. Methods In an open trial, healthy, exclusively breastfed term infants were fed 1.8 × 1010 CFU B. infantis EVC001 daily from day 7–27 postnatal (n = 34; EVC001-fed), or breastmilk alone (n = 32; control group). Fecal samples, milk samples, and weekly self-reported data were collected and analyzed for infant gut microbiome composition and function, human milk oligosaccharide composition, and fecal metabolites. 16S rRNA sequencing and shotgun metagenome sequencing provided characterization of microbial communities from birth through 60 days postnatal. Results Infants fed B. infantis EVC001 were uniformly colonized with this organism at 1011 CFU/g feces, while infants in the control group had a median total Bifidobacterium level below 10^5 CFU/g feces, despite exclusive breastfeeding. Mass spectrometry of fecal samples from B. infantis EVC001-fed infants showed that the resulting microbial community produced higher concentrations of lactate and acetate and lower excretion of HMO, while control infants showed significantly lower ability to capture and utilize these carbohydrates from human milk. Importantly, HMO content of breastmilk was not significantly different between groups and no difference was found in the gut microbiome of infants based on secretor status of mothers (presence or absence of 2’FL in breastmilk). Further, these changes were associated with reductions in taxa that have been associated with negative health outcomes including colic, asthma, eczema and allergy. Conclusions Overall, colonization with B. infantis is observed to be an effective way to restore maximal function of the infant gut microbiome to improve nutrient availability in the breastfed infant. Funding Sources This study was funded by Evolve BioSystems, Inc.

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Relationship between human milk oligosaccharides and fecal microbiome of breastfed infants

The FASEB Journal ◽

10.1096/fasebj.27.1_supplement.45.5 ◽

2013 ◽

Vol 27 (S1) ◽

Author(s):

Janet E Williams ◽

Mara A Riley ◽

Sarah L Brooker ◽

Katherine M Hunt ◽

Alexandra Szyszka ◽

...

Keyword(s):

Human Milk ◽

Human Milk Oligosaccharides ◽

Milk Oligosaccharides ◽

Fecal Microbiome ◽

Breastfed Infants

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Genetics of human gut microbiome composition

10.1101/2020.06.26.173724 ◽

2020 ◽

Cited By ~ 3

Author(s):

Alexander Kurilshikov ◽

Carolina Medina-Gomez ◽

Rodrigo Bacigalupe ◽

Djawad Radjabzadeh ◽

Jun Wang ◽

...

Keyword(s):

Association Study ◽

Gut Microbiome ◽

Genome Wide Association Study ◽

Food Preferences ◽

Microbial Composition ◽

Fecal Microbiome ◽

Microbiome Composition ◽

Genome Wide ◽

A Genome ◽

Gwas Signal

AbstractTo study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed whole-genome genotypes and 16S fecal microbiome data from 18,473 individuals (25 cohorts). Microbial composition showed high variability across cohorts: we detected only 9 out of 410 genera in more than 95% of the samples. A genome-wide association study (GWAS) of host genetic variation in relation to microbial taxa identified 30 loci affecting microbome taxa at a genome-wide significant (P<5×10-8) threshold. Just one locus, the lactase (LCT) gene region, reached study-wide significance (GWAS signal P=8.6×10−21); it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.94×10−10<P<5×10−8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization analyses identified enrichment of microbiome trait loci SNPs in the metabolic, nutrition and environment domains and indicated food preferences and diseases as mediators of genetic effects.

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Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease

PLoS ONE ◽

10.1371/journal.pone.0262317 ◽

2022 ◽

Vol 17 (1) ◽

pp. e0262317

Author(s):

Giovana S. Slanzon ◽

Benjamin J. Ridenhour ◽

Dale A. Moore ◽

William M. Sischo ◽

Lindsay M. Parrish ◽

...

Keyword(s):

Health Status ◽

Relative Abundance ◽

Gastrointestinal Disease ◽

Bifidobacterium Longum ◽

Dairy Calves ◽

Rrna Gene ◽

Probiotic Properties ◽

Fecal Samples ◽

Fecal Microbiome ◽

Microbiome Composition

Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microbiome. Fecal samples were collected from calves (n = 167) of different breeds (Holstein, Jersey, Jersey-cross and beef-cross) from 4–21 d of age. Daily clinical evaluations assessed health status. Calves with loose or watery feces were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to behavior. Calves with normal or semiformed feces and no clinical illness were classified as healthy (H). One hundred and three fecal samples were obtained from consistently healthy calves and 64 samples were from calves with diarrhea (n = 39 BS; n = 25 DS). The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Differences were identified by a linear-mixed effects model with a negative binomial error. DS and Jersey calves had a higher relative abundance of Streptococcus gallolyticus relative to H Holstein calves. In addition, DS calves had a lower relative abundance of Bifidobacterium longum and an enrichment of Escherichia coli. Species of the genus Lactobacillus, such as an unclassified Lactobacillus, Lactobacillus reuteri, and Lactobacillus salivarius were enriched in calves with GI disease. Moreover, we created a model to predict GI disease based on the fecal microbiome composition. The presence of Eggerthella lenta, Bifidobacterium longum, and Collinsella aerofaciens were associated with a healthy clinical outcome. Although lactobacilli are often associated with beneficial probiotic properties, the presence of E. coli and Lactobacillus species had the highest coefficients positively associated with GI disease prediction. Our results indicate that there are differences in the fecal microbiome of calves associated with GI disease severity and breed specificities.

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Weaning age and its effect on the development of the swine gut microbiome and resistome

10.1101/2021.05.20.444551 ◽

2021 ◽

Author(s):

Devin B Holman ◽

Katherine E Gzyl ◽

Kathy T Mou ◽

Heather K Allen

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Carbohydrate Active Enzymes ◽

Fecal Microbiome ◽

Shotgun Metagenomic Sequencing ◽

Swine Operations ◽

Weaning Age

Piglets are often weaned between 19 and 22 d of age in North America although in some swine operations this may occur at 14 d or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sow's milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. In this study, pigs were weaned at either 14, 21, or 28 d of age and fecal samples collected 21 times from d 4 (neonatal) through to marketing at d 140. The fecal microbiome was characterized using 16S rRNA gene and shotgun metagenomic sequencing. The fecal microbiome of all piglets shifted significantly three to seven days post-weaning with an increase in microbial diversity. Several Prevotella spp. increased in relative abundance immediately after weaning as did butyrate-producing species such as Butyricicoccus porcorum, Faecalibacterium prausnitzii, and Megasphaera elsdenii. Within 7 days of weaning, the gut microbiome of pigs weaned at 21 and 28 days of age resembled that of pigs weaned at 14 d. Resistance genes to most antimicrobial classes decreased in relative abundance post-weaning with the exception of those conferring resistance to tetracyclines and macrolides-lincosamides-streptogramin B. The relative abundance of microbial carbohydrate-active enzymes (CAZymes) changed significantly in the post-weaning period with an enrichment of CAZymes involved in degradation of plant-derived polysaccharides. These results demonstrate that pigs tend to have a more similar microbiome as they age and that weaning age has only a temporary effect on the gut microbiome.

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Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes

10.1101/2021.06.04.447087 ◽

2021 ◽

Author(s):

Lauren Tso ◽

Kevin S Bonham ◽

Alyssa Fishbein ◽

Sophie Rowland ◽

Vanja Klepac-Ceraj ◽

...

Keyword(s):

Human Milk ◽

Bifidobacterium Longum ◽

Gene Clusters ◽

Species Group ◽

Human Breast Milk ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Specific Primers ◽

Breastfed Infants ◽

Shotgun Metagenomic Sequencing

Bifidobacterium longum subsp. infantis (B. infantis) is one of few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis, by molecular methods. These two organisms are classified in the same species group as B. infantis but do not share the ability to metabolize human milk oligosaccharides (HMOs). Here, we compared HMO-metabolizing genes across different Bifidobacterium genomes to develop B. infantis specific primers and determine if they alone can be used to quickly characterize B. infantis with shotgun metagenomic sequencing data. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, used this characterization to test for its prevalence in infants, and validated the results using the B. infantis-specific primers. By examining stool samples from a cohort of US children and pregnant women using shotgun metagenomic sequencing, we observed that only 18 of 204 (8.8%) of children under 2 years old harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.

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