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Edwards CA, Van Loo-Bouwman CA, Van Diepen JA, Schoemaker MH, Ozanne SE, Venema K, Stanton C, Marinello V, Rueda R, Flourakis M, Gil A, Van der Beek EM. A systematic review of breast milk microbiota composition and the evidence for transfer to and colonisation of the infant gut. Benef Microbes 2022; 13:365-382. [PMID: 36377578 DOI: 10.3920/bm2021.0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The intestinal microbiota plays a major role in infant health and development. However, the role of the breastmilk microbiota in infant gut colonisation remains unclear. A systematic review was performed to evaluate the composition of the breastmilk microbiota and evidence for transfer to/colonisation of the infant gut. Searches were performed using PUBMED, OVID, LILACS and PROQUEST from inception until 18th March 2020 with a PUBMED update to December 2021. 88 full texts were evaluated before final critique based on study power, sample contamination avoidance, storage, purification process, DNA extraction/analysis, and consideration of maternal health and other potential confounders. Risk of skin contamination was reduced mainly by breast cleaning and rejecting the first milk drops. Sample storage, DNA extraction and bioinformatics varied. Several studies stored samples under conditions that may selectively impact bacterial DNA preservation, others used preculture reducing reliability. Only 15 studies, with acceptable sample size, handling, extraction, and bacterial analysis, considered transfer of bacteria to the infant. Three reported bacterial transfer from infant to breastmilk. Despite consistent evidence for the breastmilk microbiota, and recent studies using improved methods to investigate factors affecting its composition, few studies adequately considered transfer to the infant gut providing very little evidence for effective impact on gut colonisation.
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Affiliation(s)
- C A Edwards
- Human Nutrition, School of Medicine, Dentistry, and Nursing, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, 84 Castle St, Glasgow G4 0SF, United Kingdom
| | - C A Van Loo-Bouwman
- Yili Innovation Center Europe, Bronland 12 E-1, 6708 WH Wageningen, the Netherlands
| | - J A Van Diepen
- Medical and Scientific Affairs, Reckitt|Mead Johnson Nutrition Institute, Middenkampweg 2, 6545 CJ Nijmegen, the Netherlands
| | - M H Schoemaker
- Medical and Scientific Affairs, Reckitt|Mead Johnson Nutrition Institute, Middenkampweg 2, 6545 CJ Nijmegen, the Netherlands
| | - S E Ozanne
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, P.O. Box 289, Cambridge CB2 0QQ, United Kingdom
| | - K Venema
- Department of Human Biology, Centre for Healthy Eating & Food Innovation, Maastricht University - Campus Venlo, P.O. Box 8, 5900 AA Venlo, the Netherlands
| | - C Stanton
- Teagasc Moorepark Food Research Centre, and APC Microbiome Ireland, Cork, Ireland
| | - V Marinello
- Human Nutrition, School of Medicine, Dentistry, and Nursing, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, 84 Castle St, Glasgow G4 0SF, United Kingdom
| | - R Rueda
- R&D Department, Abbott Nutrition, Cam. de Purchil, 68, 18004 Granada, Spain
| | - M Flourakis
- ILSI Europe a.i.s.b.l., E. Mounierlaan 83, 1200 Brussels, Belgium; correspondence has been taken over by C.-Y. Chang of ILSI Europe
| | - A Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, Institute of Nutrition and Food Technology 'José Mataix,' Biomedical Research Centre, University of Granada, and Instituto de Investigación Biosanitaria ibs Granada, Avda. del Conocimiento s/n, 18100, Armilla, Grenada, Spain
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - E M Van der Beek
- Department of Pediatrics, University Medical Centre Groningen, University of Groningen, Postbus 30.001, 9700 RB Groningen, the Netherlands
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands
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Sanjulián L, Lamas A, Barreiro R, Cepeda A, Fente CA, Regal P. Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum. Nutrients 2021; 13:2414. [PMID: 34371924 PMCID: PMC8308733 DOI: 10.3390/nu13072414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/27/2022] Open
Abstract
The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.
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Affiliation(s)
| | - Alexandre Lamas
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Veterinary Science, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (L.S.); (R.B.); (A.C.); (C.A.F.)
| | | | | | | | - Patricia Regal
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Veterinary Science, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (L.S.); (R.B.); (A.C.); (C.A.F.)
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Lopez Leyva L, Brereton NJ, Koski KG. Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis. Comput Struct Biotechnol J 2020; 19:121-133. [PMID: 33425245 PMCID: PMC7770459 DOI: 10.1016/j.csbj.2020.11.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Human milk is the ideal food for infants due to its unique nutritional and immune properties, and more recently human milk has also been recognized as an important source of bacteria for infants. However, a substantial amount of fundamental human milk microbiome information remains unclear, such as the origin, composition and function of the community and its members. There is emerging evidence to suggest that the diversity and composition of the milk microbiome might differ between lactation stages, due to maternal factors and diet, agrarian and urban lifestyles, and geographical location. The evolution of the methods used for studying milk microbiota, transitioning from culture dependent-approaches to include culture-independent approaches, has had an impact on findings and, in particular, primer selection within 16S rRNA gene barcoding studies have led to discrepancies in observed microbiota communities. Here, the current state-of-the-art is reviewed and emerging frontiers essential to improving our understanding of the human milk microbiome are considered.
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Affiliation(s)
- Lilian Lopez Leyva
- School of Human Nutrition, McGill University, Macdonald Stewart Building, 21111 Lakeshore Road, Ste-Anne de Bellevue, QC H9X 3V9, Canada
| | - Nicholas J.B. Brereton
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Kristine G. Koski
- School of Human Nutrition, McGill University, Macdonald Stewart Building, 21111 Lakeshore Road, Ste-Anne de Bellevue, QC H9X 3V9, Canada
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Quin C, Gibson DL. Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants. Gut Microbes 2020; 11:1143-1171. [PMID: 32249675 PMCID: PMC7524360 DOI: 10.1080/19490976.2020.1736973] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.
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Affiliation(s)
- Candice Quin
- Department of Biology, University of British Columbia, Kelowna, Canada
| | - Deanna L. Gibson
- Department of Biology, University of British Columbia, Kelowna, Canada,Department of Medicine, University of British Columbia, Kelowna, Canada,CONTACT Deanna L. Gibson Department of Biology, University of British Columbia, Okanagan Campus, ASC 386, 3187 University Way, Kelowna, BCV1V 1V7, Canada
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Liu J, Zhu Y, Jay-Russell M, Lemay DG, Mills DA. Reservoirs of antimicrobial resistance genes in retail raw milk. MICROBIOME 2020; 8:99. [PMID: 32591006 PMCID: PMC7320593 DOI: 10.1186/s40168-020-00861-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/11/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic resistome in both raw and processed milk, we systematically analyzed 2034 retail milk samples including unpasteurized milk and pasteurized milk via vat pasteurization, high-temperature-short-time pasteurization, and ultra-pasteurization from the United States using complementary culture-based, 16S rRNA gene, and metagenomic sequencing techniques. RESULTS Raw milk samples had the highest prevalence of viable bacteria which were measured as all aerobic bacteria, coliform, and Escherichia coli counts, and their microbiota was distinct from other types of milk. 16S rRNA gene sequencing revealed that Pseudomonadaceae dominated raw milk with limited levels of lactic acid bacteria. Among all milk samples, the microbiota remained stable with constant bacterial populations when stored at 4 °C. In contrast, storage at room temperature dramatically enriched the bacterial populations present in raw milk samples and, in parallel, significantly increased the richness and abundance of ARGs. Metagenomic sequencing indicated raw milk possessed dramatically more ARGs than pasteurized milk, and a conjugation assay documented the active transfer of blaCMY-2, one ceftazidime resistance gene present in raw milk-borne E. coli, across bacterial species. The room temperature-enriched resistome differed in raw milk from distinct geographic locations, a difference likely associated with regionally distinct milk microbiota. CONCLUSION Despite advertised "probiotic" effects, our results indicate that raw milk microbiota has minimal lactic acid bacteria. In addition, retail raw milk serves as a reservoir of ARGs, populations of which are readily amplified by spontaneous fermentation. There is an increased need to understand potential food safety risks from improper transportation and storage of raw milk with regard to ARGs. Video Abstract.
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Affiliation(s)
- Jinxin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
- Foods for Health Institute, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Yuanting Zhu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
- Foods for Health Institute, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Michele Jay-Russell
- Western Center for Food Safety, University of California, Davis, Davis, CA, 95616, USA
| | - Danielle G Lemay
- USDA ARS Western Human Nutrition Research Center, 430 West Health Sciences Dr, Davis, CA, 95616, USA
- Genome Center, University of California, 451 Health Sciences Dr., Davis, California, 95616, USA
- Department of Nutrition, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - David A Mills
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
- Foods for Health Institute, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
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Treven P, Mahnič A, Rupnik M, Golob M, Pirš T, Matijašić BB, Lorbeg PM. Evaluation of Human Milk Microbiota by 16S rRNA Gene Next-Generation Sequencing (NGS) and Cultivation/MALDI-TOF Mass Spectrometry Identification. Front Microbiol 2019; 10:2612. [PMID: 31803156 PMCID: PMC6872673 DOI: 10.3389/fmicb.2019.02612] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
The aim of the present study was to characterize human milk microbiota (HMM) with 16S rRNA gene amplicon next-generation sequencing and cultivation/matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) identification approaches. We analyzed 31 human milk samples from healthy Slovenian mothers. To check the accuracy of MALDI-TOF MS identification, several colonies representing most abundant genera and those, which could not be reliably identified by MALDI-TOF, were subjected to Sanger sequencing of their 16S rRNA gene. We showed that cultivation/MALDI-TOF MS was a suitable tool for culture-dependent determination of HMM. With both approaches, Staphylococcus and Streptococcus were found as predominant genera in HMM and the abundance of Staphylococcus was associated with decreased microbial diversity. In addition, we characterized factors that might influence HMM. The use of a breast pump was significantly associated with composition of HMM, lower microbial load, and higher abundance of cultivable staphylococci. Moreover, our study suggests that administration of probiotics to the suckling infant might influence HMM by increased abundance of lactobacilli and the presence of viable probiotic bacteria in human milk. However, since our study was observational with relatively small sample size, more targeted studies are needed to study possible transfer of probiotics to the mammary gland via an external route and the physiological relevance of these events.
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Affiliation(s)
- Primož Treven
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
| | - Aleksander Mahnič
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Majda Golob
- Faculty of Veterinary Medicine, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Tina Pirš
- Faculty of Veterinary Medicine, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Bojana Bogovič Matijašić
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Mohar Lorbeg
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
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Liu J, Taft DH, Maldonado-Gomez MX, Johnson D, Treiber ML, Lemay DG, DePeters EJ, Mills DA. The fecal resistome of dairy cattle is associated with diet during nursing. Nat Commun 2019; 10:4406. [PMID: 31562300 PMCID: PMC6765000 DOI: 10.1038/s41467-019-12111-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/24/2019] [Indexed: 01/07/2023] Open
Abstract
Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.
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Affiliation(s)
- Jinxin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- Foods for Health Institute, University of California, Davis, California, One Shields Ave., Davis, CA, 95616, USA
| | - Diana H Taft
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- Foods for Health Institute, University of California, Davis, California, One Shields Ave., Davis, CA, 95616, USA
| | - Maria X Maldonado-Gomez
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- Foods for Health Institute, University of California, Davis, California, One Shields Ave., Davis, CA, 95616, USA
| | - Daisy Johnson
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- Foods for Health Institute, University of California, Davis, California, One Shields Ave., Davis, CA, 95616, USA
| | - Michelle L Treiber
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
- USDA ARS Western Human Nutrition Research Center, 430 West Health Sciences Dr., Davis, CA, 95616, USA
| | - Danielle G Lemay
- USDA ARS Western Human Nutrition Research Center, 430 West Health Sciences Dr., Davis, CA, 95616, USA
- Genome Center, University of California, 451 Health Science Dr., Davis, CA, 95616, USA
- Department of Nutrition, University of California, Davis, California, Davis, CA, 95616, USA
| | - Edward J DePeters
- Department of Animal Science, University of California, Davis, California, Davis, CA, 95616, USA
| | - David A Mills
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA.
- Foods for Health Institute, University of California, Davis, California, One Shields Ave., Davis, CA, 95616, USA.
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, California, One Shields Ave., Davis, CA, 95616, USA.
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Ruiz L, García-Carral C, Rodriguez JM. Unfolding the Human Milk Microbiome Landscape in the Omics Era. Front Microbiol 2019; 10:1378. [PMID: 31293535 PMCID: PMC6604669 DOI: 10.3389/fmicb.2019.01378] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/03/2019] [Indexed: 12/31/2022] Open
Abstract
Studies conducted in the last years have demonstrated that human milk represents a continuous supply of beneficial bacteria to the infant gut, which contribute to the maturation of the digestive and immune functions in the developing infant. Nevertheless, the origin of bacterial populations in milk is not fully understood yet and they have been proposed to originate from maternal skin, infant’s mouth, and (or) endogenously, from the maternal digestive tract through a mechanism involving immune cells. Understanding the composition, functions and assembly of the human milk microbiota has important implications not only for the infant gut microbiota establishment, but also for the mammary health since dysbiosis in the milk bacteria may lead to mastitis. Besides, host, microbial, medical and environmental factors may affect the composition of the human milk microbiome, with implications for the mother-infant health. Application of both culture-dependent and -independent techniques to assess the milk microbiome faces some practical limitations but, together, have allowed providing novel and complementary views on its origin, composition and functioning as summarized in this minireview. In the next future, the application of the ultimate advances in next-generation sequencing and omics approaches, including culturomics, will allow a detailed and comprehensive understanding of the composition and functions of these microbial communities, including their interactions with other milk components, expanding the opportunities to design novel microbiome-based modulation strategies for this ecosystem.
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Affiliation(s)
- Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - Cristina García-Carral
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain
| | - Juan Miguel Rodriguez
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain
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Feng XW, Ding WP, Xiong LY, Guo L, Sun JM, Xiao P. Recent Advancements in Intestinal Microbiota Analyses: A Review for Non-Microbiologists. Curr Med Sci 2018; 38:949-961. [PMID: 30536055 DOI: 10.1007/s11596-018-1969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 06/12/2018] [Indexed: 02/06/2023]
Abstract
Microbial constituents naturally inhabiting the gastrointestinal tract may influence the homeostasis of the gut environment. The presence or overabundance of some bacterial taxa has been reported to be associated with complex diseases, and the metabolites of certain bacteria may contribute to diverse disorders by influencing signaling pathways. Therefore, the study of gut microbial population has emerged as a crucial field and a new potential area of clinical significance. Advances in the methods of microbiota analysis have shed light upon the details including species diversity, microfloral activities as well as the entire gut microbiota. Nevertheless, comprehensive reviews on this subject are still limited. For elucidating the appropriate selection strategy of the methods to address a particular research question, we comprehensively reviewed the continuously improving technologies, classical to newly developed, and dissected their relative advantages and drawbacks. In addition, aiming at the rapidly advancing next-generation sequencing, we enumerated the improvements in mainstream platforms and made the horizontal and vertical comparison among them. Additionally, we demonstrated the four main -omics methods, which may provide further mechanistic insights into the role of microbiota, to propel phylotyping analysis to functional analysis.
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Affiliation(s)
- Xiao-Wei Feng
- Department of Psychiatry, Wuhan Youfu Hospital, Wuhan, 430050, China
| | - Wen-Ping Ding
- Department of Ultrasound, Wuhan Women and Children's Health Care Center, Wuhan, 430016, China
| | - Ling-Yun Xiong
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Liang Guo
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jia-Ming Sun
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Peng Xiao
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Damaceno QS, Souza JP, Nicoli JR, Paula RL, Assis GB, Figueiredo HC, Azevedo V, Martins FS. Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum. Probiotics Antimicrob Proteins 2018; 9:371-379. [PMID: 28374172 DOI: 10.1007/s12602-017-9270-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Several studies have demonstrated a diversity of bacterial species in human milk, even in aseptically collected samples. The present study evaluated potential probiotic bacteria isolated from human milk and associated maternal variables. Milk samples were collected from 47 healthy women and cultured on selective and universal agar media under aerobic and anaerobic conditions. Bacterial isolates were counted and identified by Biotyper Matrix-Assisted Laser Desorption Ionization-Time of Flight mass spectrometry and then tested for probiotic properties. Total bacteria in human milk ranged from 1.5 to 4.0 log10 CFU/mL. The higher bacterial counts were found in colostrum (mean = 3.9 log10 CFU/mL, 95% CI 3.14-4.22, p = 0.00001). The most abundant species was Staphylococcus epidermidis (n = 76). The potential probiotic candidates were Lactobacillus gasseri (n = 4), Bifidobacterium breve (n = 1), and Streptococcus salivarius (n = 4). Despite the small sample size, L. gasseri was isolated only in breast milk from mothers classified into a normal weight range and after a vaginally delivered partum. No potential probiotics showed antagonism against pathogens, but all of them agglutinated different pathogens. Nine bacterial isolates belonging to the species L. gasseri, B. breve, and S. salivarius were selected as potential probiotics. The present study confirms the presence in breast milk of a bacterial microbiota that could be the source of potential probiotic candidates to be used in the formula of simulated maternal milk.
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Affiliation(s)
- Quésia S Damaceno
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jaqueline P Souza
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jacques R Nicoli
- Laboratory of Microbial Ecology and Physiology, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Raquel L Paula
- Neonatology, Hospital Sofia Feldman, Belo Horizonte, MG, Brazil
| | - Gabriela B Assis
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Henrique C Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flaviano S Martins
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Laboratory of Microbial Ecology and Physiology, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Laboratório de Agentes Bioterapêuticos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, C.P. 486, Pampulha - Campus UFMG, Belo Horizonte, MG, 31270-901, Brazil.
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Bardanzellu F, Fanos V, Strigini FAL, Artini PG, Peroni DG. Human Breast Milk: Exploring the Linking Ring Among Emerging Components. Front Pediatr 2018; 6:215. [PMID: 30131948 PMCID: PMC6091001 DOI: 10.3389/fped.2018.00215] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022] Open
Abstract
Maternal breast milk (BM) is a complex and unique fluid that evolution adapted to satisfy neonatal needs; in addition to classical nutrients, it contains several bioactive components. BM characteristically shows inter-individual variability, modifying its composition during different phases of lactation. BM composition, determining important consequences on neonatal gut colonization, influences both short and long-term development. Maternal milk can also shape neonatal microbiota, through its glycobiome rich in Lactobacilli spp. and Bifidobacteria spp. Therefore, neonatal nourishment during the first months of life seems the most important determinant of individual's outcomes. Our manuscript aims to provide new evidence in the characterization of BM metabolome and microbiome, and its comparison to formula milk, allowing the evaluation of each nutrient's influence on neonatal metabolism. This result very interesting since potentially offers an innovative approach to investigate the complex relationship between BM components and infant's health, also providing the chance to intervene in a sartorial way on diet composition, according to the nutritional requests. Future research, integrating metabolomics, microbiomics and stem cells knowledge, could make significant steps forward in understanding BM extraordinary properties and functions.
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Affiliation(s)
- Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Neonatal Pathology and Neonatal Section, Azienda Ospedaliera Universitaria di Cagliari, University of Cagliari, Cagliari, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Neonatal Pathology and Neonatal Section, Azienda Ospedaliera Universitaria di Cagliari, University of Cagliari, Cagliari, Italy
| | | | - Paolo G Artini
- Gynecology and Obstetrics, Università degli Studi di Pisa, Pisa, Italy
| | - Diego G Peroni
- Section of Pediatric, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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12
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Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters. Sci Rep 2017; 7:11230. [PMID: 28894126 PMCID: PMC5593852 DOI: 10.1038/s41598-017-10244-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/07/2017] [Indexed: 12/19/2022] Open
Abstract
Sound and timely microbial gut colonization completes newborn’s healthy metabolic programming and manifests in infant appropriate growth and weight development. Feces, collected at 3, 30, and 90 days after birth from 60 breastfed Slovenian newborns, was submitted to microbial DNA extraction and qPCR quantification of selected gut associated taxa. Multivariate regression analysis was applied to evaluate microbial dynamics with respect to infant demographic, environmental, clinical characteristics and first year growth data. Early microbial variability was marked by the proportion of Bacilli, but diminished and converged in later samples, as bifidobacteria started to prevail. The first month proportions of enterococci were associated with maternity hospital locality and supplementation of breastfeeding with formulae, while Enterococcus faecalis proportion reflected the mode of delivery. Group Bacteroides-Prevotella proportion was associated with infant weight and ponderal index at first month. Infant mixed feeding pattern and health issues within the first month revealed the most profound and extended microbial perturbations. Our findings raise concerns over the ability of the early feeding supplementation to emulate and support the gut microbiota in a way similar to the exclusively breastfed infants. Additionally, practicing supplementation beyond the first month also manifested in higher first year weight and weight gain Z-score.
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Williams JE, Carrothers JM, Lackey KA, Beatty NF, York MA, Brooker SL, Shafii B, Price WJ, Settles ML, McGuire MA, McGuire MK. Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women. J Nutr 2017; 147:1739-1748. [PMID: 28724659 PMCID: PMC5572491 DOI: 10.3945/jn.117.248864] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/13/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
Background: The human milk microbiome has been somewhat characterized, but little is known about changes over time and relations with maternal factors such as nutrient intake.Objective: We sought to characterize the human milk microbiome and described associations with maternal nutrient intake, time postpartum, delivery mode, and body mass index (BMI; in kg/m2).Methods: Milk samples (n = 104) and 24-h diet recalls were collected 9 times from 21 healthy lactating women from day 2 to 6 mo postpartum. Women were classified by BMI as healthy weight (<25) or overweight or obese (≥25). Bacterial taxa were characterized with the use of the high-throughput sequencing of the 16S ribosomal RNA gene.Results: The milk microbiome was relatively constant over time, although there were small changes in some of the lesser-abundant genera. Relative abundances of several taxa were associated with BMI, delivery mode, and infant sex. For instance, overweight and obese mothers produced milk with a higher relative abundance of Granulicatella than did healthy-weight women (1.8% ± 0.6% compared with 0.4% ± 0.2%, respectively; P < 0.05). Relative abundances of several bacterial taxa were also associated with variations in maternal dietary intake. For example, intakes of saturated fatty acids (rs = -0.59; P = 0.005) and monounsaturated fatty acids (rs = -0.46; P = 0.036) were inversely associated with the relative abundance of Corynebacterium; total carbohydrates (rs = -0.54; P = 0.011), disaccharides (rs = -0.47; P = 0.031), and lactose (rs = -0.51; P = 0.018) were negatively associated with Firmicutes; and protein consumption was positively correlated with the relative abundance of Gemella (rs = 0.46; P = 0.037).Conclusions: Factors associated with variations in the human milk microbiome are complex and may include maternal nutrient intake, maternal BMI, delivery mode, and infant sex. Future studies designed to investigate the relation between maternal nutrient intake and the milk microbiome should strive to also evaluate dietary supplement usage and analyze the collected milk for its nutrient content.
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Affiliation(s)
- Janet E Williams
- Department of Animal and Veterinary Sciences, .,Program in Bioinformatics and Computational Biology, and
| | | | | | | | | | - Sarah L Brooker
- Department of Animal and Veterinary Sciences,,Program in Bioinformatics and Computational Biology, and
| | - Bahman Shafii
- Statistical Programs, College of Agricultural and Life Sciences, University of Idaho, Moscow, ID
| | - William J Price
- Statistical Programs, College of Agricultural and Life Sciences, University of Idaho, Moscow, ID
| | - Matthew L Settles
- Bioinformatics Core Facility in the Genome Center, University of California, Davis, Davis, CA
| | | | - Michelle K McGuire
- School of Biological Sciences and .,Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA; and
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14
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Turck D, Bresson JL, Burlingame B, Dean T, Fairweather-Tait S, Heinonen M, Hirsch-Ernst KI, Mangelsdorf I, McArdle HJ, Naska A, Neuhäuser-Berthold M, Nowicka G, Pentieva K, Sanz Y, Stern M, Tomé D, Van Loveren H, Vinceti M, Willatts P, Martin A, Strain JJ, Siani A. Lactobacillus fermentum CECT 5716 and a reduction of the Staphylococcus load in breast milk which reduces the risk of infectious mastitis: evaluation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006. EFSA J 2017; 15:e04917. [PMID: 32625577 PMCID: PMC7010029 DOI: 10.2903/j.efsa.2017.4917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Following an application from Biosearch Life, submitted for authorisation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 via the Competent Authority of France, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on the scientific substantiation of a health claim related to Lactobacillus fermentum CECT 5716 and decreases the Staphylococcus load in breast milk. High Staphylococcus load in breast milk is a risk factor for infectious mastitis. The scope of the application was proposed to fall under a health claim referring to disease risk reduction. The Panel considers that Lactobacillus fermentum CECT 5716 is sufficiently characterised. In the context of this application, the Staphylococcus load in breast milk can be considered a risk factor for the development of infectious mastitis, as long as evidence is provided that the consumption of Lactobacillus fermentum CECT 5716 reduces the Staphylococcus load in breast milk as well as the incidence of infectious mastitis. Three human intervention studies investigated the effect of Lactobacillus fermentum CECT 5716 on the Staphylococcus load of breast milk in lactating women. One of these studies was conducted in lactating women free of infectious mastitis at baseline. The Panel considers that no conclusions can be drawn from this study for the scientific substantiation of the claim owing to important methodological limitations. The other two studies were conducted in lactating women with infectious mastitis and, therefore, the effect of the intervention on the incidence of infectious mastitis cannot be assessed. The Panel concludes that a cause and effect relationship has not been established between the consumption of Lactobacillus fermentum CECT 5716 and a reduction of the Staphylococcus load in breast milk which reduces the risk of infectious mastitis.
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15
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Perinatal Microbiomes' Influence on Preterm Birth and Preterms' Health: Influencing Factors and Modulation Strategies. J Pediatr Gastroenterol Nutr 2016; 63:e193-e203. [PMID: 27019409 DOI: 10.1097/mpg.0000000000001196] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microbial communities inhabiting the human host play important roles in maintaining health status, including reproduction and early life programming, which is particularly important in the context of preterm neonates' health. Preterm birth (PTB) is often the result of a microbial dysbiosis or infection. In addition, preterm neonates experience different levels of organ immaturity and an abnormal gut microbiota establishment, as compared to full-term neonates. This exacerbates their developmental problems and can have negative consequences at systemic level. In addition, preterm babies are commonly exposed to delayed enteral feeding and hospital environments, which increases the risk of short- and long-term health problems. Some of these clinical conditions, such as necrotizing enterocolitis or sepsis, may be life threatening, whereas others may translate into life-long conditions, including cognitive problems. Increasing scientific interest has focused on understanding developmental problems in preterm neonates related to abnormalities in the settlement of their microbial communities, with the final goal of selecting appropriate microbiome-targeted strategies (eg, probiotics), to reduce preterm health risks and improve overall quality of life.This review aims to summarize current knowledge on microbiological factors influencing PTB initiation and gastrointestinal development, and on the health consequences to the preterm neonate. Scientific evidences on dietary strategies reducing PTB incidence and minimizing sequelae in this particularly sensitive human group subpopulation are also discussed.
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16
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Fitzstevens JL, Smith KC, Hagadorn JI, Caimano MJ, Matson AP, Brownell EA. Systematic Review of the Human Milk Microbiota. Nutr Clin Pract 2016; 32:354-364. [PMID: 27679525 DOI: 10.1177/0884533616670150] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Human milk-associated microbes are among the first to colonize the infant gut and may help to shape both short- and long-term infant health outcomes. We performed a systematic review to characterize the microbiota of human milk. Relevant primary studies were identified through a comprehensive search of PubMed (January 1, 1964, to June 31, 2015). Included studies were conducted among healthy mothers, were written in English, identified bacteria in human milk, used culture-independent methods, and reported primary results at the genus level. Twelve studies satisfied inclusion criteria. All varied in geographic location and human milk collection/storage/analytic methods. Streptococcus was identified in human milk samples in 11 studies (91.6%) and Staphylococcus in 10 (83.3%); both were predominant genera in 6 (50%). Eight of the 12 studies used conventional ribosomal RNA (rRNA) polymerase chain reaction (PCR), of which 7 (87.5%) identified Streptococcus and 6 (80%) identified Staphylococcus as present. Of these 8 studies, 2 (25%) identified Streptococcus and Staphylococcus as predominant genera. Four of the 12 studies used next-generation sequencing (NGS), all of which identified Streptococcus and Staphylococcus as present and predominant genera. Relative to conventional rRNA PCR, NGS is a more sensitive method to identify/quantify bacterial genera in human milk, suggesting the predominance of Streptococcus and Staphylococcus may be underestimated in studies using older methods. These genera, Streptococcus and Staphylococcus, may be universally predominant in human milk, regardless of differences in geographic location or analytic methods. Primary studies designed to evaluate the effect of these 2 genera on short- and long-term infant outcomes are warranted.
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Affiliation(s)
- John L Fitzstevens
- 1 Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, USA
| | - Kelsey C Smith
- 2 Connecticut Human Milk Research Center, Connecticut Children's Medical Center, Hartford, Connecticut, USA.,3 Division of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - James I Hagadorn
- 2 Connecticut Human Milk Research Center, Connecticut Children's Medical Center, Hartford, Connecticut, USA.,3 Division of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut, USA.,4 Department of Pediatrics, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Melissa J Caimano
- 5 Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.,6 Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Adam P Matson
- 3 Division of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut, USA.,4 Department of Pediatrics, University of Connecticut School of Medicine, Farmington, Connecticut, USA.,7 Department of Immunology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Elizabeth A Brownell
- 2 Connecticut Human Milk Research Center, Connecticut Children's Medical Center, Hartford, Connecticut, USA.,3 Division of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut, USA.,4 Department of Pediatrics, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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17
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Obermajer T, Pogačić T. Commentary: Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation. Front Microbiol 2016; 7:1281. [PMID: 27581429 PMCID: PMC4987343 DOI: 10.3389/fmicb.2016.01281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 08/03/2016] [Indexed: 12/30/2022] Open
Affiliation(s)
- Tanja Obermajer
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana Domžale, Slovenia
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Affiliation(s)
- William A Banks
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington; and Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98108
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Obermajer T, Lipoglavšek L, Tompa G, Treven P, Lorbeg PM, Matijašić BB, Rogelj I. Correction: Colostrum of Healthy Slovenian Mothers: Microbiota Composition and Bacteriocin Gene Prevalence. PLoS One 2015; 10:e0132201. [PMID: 26120836 PMCID: PMC4488312 DOI: 10.1371/journal.pone.0132201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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