1
|
Silva JFM, Alonso BV, Almeida PAA, Barbosa IV, Braga de Paula OA, Barbosa LR, Bruno LM, Menezes LDM, Silva MR, Costa GMD, Rodarte MP, Ribeiro JB. Searching for antibiotic-susceptible bioprotective lactic acid bacteria to control dangerous biological agents in artisanal cheese. Food Microbiol 2025; 130:104762. [PMID: 40210393 DOI: 10.1016/j.fm.2025.104762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 02/24/2025] [Accepted: 02/28/2025] [Indexed: 04/12/2025]
Abstract
Minas artisanal cheese (MAC) samples (n = 59) from 16 municipalities across five traditional MAC-producing regions in Brazil were used to prospect antibiotic-susceptible protective lactic acid bacteria (LAB) against three pathogenic bacteria found in the MAC. From 291 LAB isolates, 84 genetically diverse strains were selected via rep-PCR. MALDI-TOF identification revealed multiple species, predominantly Enterococcus faecalis (n = 37), Enterococcus faecium (n = 21), Lactiplantibacillus plantarum (n = 5) and Lacticaseibacillus rhamnosus (n = 3). The antagonistic activity of these strains was evaluated against Enterococcus faecalis ATCC 29212, Listeria monocytogenes ATCC 5779, and Escherichia coli O157:H7 using spot-on-lawn assays. Several strains showed strong inhibitory effects against E. coli and L. monocytogenes, with halo/colony ratios reaching 4.86 and 4.47, respectively. No antimicrobial peptide producing strain was observed. Antibiotic susceptibility was tested against nine antibiotics, and five strains were susceptible to all antibiotics, while 53 strains were susceptible to 5-8 antibiotics. However, five strains were resistant to all antibiotics, showing the highest resistance to gentamicin (66.7%), cotrimoxazole (58.3%), and streptomycin (57.2%). Resistance genes (aacA-aphD, ermA/B, tetM/O/K/L/S, blaZ, and vanA/B) were screened, and 40 strains harbored at least one gene. Taken together, these results revealed three antibiotic-susceptible bioprotective lactobacilli (L. rhamnosus 52, L. plantarum 177, and L. plantarum 272G) as superior strains, whose efficacy in eliminating E. coli O157 and Listeria monocytogenes in the milk matrix between 7- and 21-days post-inoculation was confirmed. These findings confirm the potential of these autochthonous lactobacilli to improve the safety of dairy, paving the way for their applications in product development in future projects.
Collapse
Affiliation(s)
- Joice Fátima Moreira Silva
- Postgraduate Program in Veterinary Sciences, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.
| | - Bruna Vieira Alonso
- Postgraduate Program in Science and Technology of Milk and Dairy Products, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
| | | | - Isabela Vieira Barbosa
- Postgraduate Program in Science and Technology of Milk and Dairy Products, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
| | | | - Letícia Ribeiro Barbosa
- Postgraduate Pharmaceutical Sciences Program, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
| | - Laura Maria Bruno
- Brazilian Agricultural Research Corporation, Fortaleza, CE, 60511-110, Brazil.
| | | | - Márcio Roberto Silva
- Brazilian Agricultural Research Corporation, Juiz de Fora, MG, 36038-330, Brazil.
| | - Geraldo Márcio da Costa
- Postgraduate Program in Veterinary Sciences, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.
| | - Mirian Pereira Rodarte
- Postgraduate Program in Science and Technology of Milk and Dairy Products, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
| | - João Batista Ribeiro
- Brazilian Agricultural Research Corporation, Juiz de Fora, MG, 36038-330, Brazil.
| |
Collapse
|
2
|
Du H, Li K, Guo W, Na M, Zhang J, Na R. Maternal Roughage Sources Influence the Gastrointestinal Development of Goat Kids by Modulating the Colonization of Gastrointestinal Microbiota. Animals (Basel) 2025; 15:393. [PMID: 39943163 PMCID: PMC11815875 DOI: 10.3390/ani15030393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 01/27/2025] [Accepted: 01/28/2025] [Indexed: 02/16/2025] Open
Abstract
During pregnancy and lactation, maternal nutrition is linked to the full development of offspring and may have long-term or lifelong effects. However, the influence of the doe's diet on the gastrointestinal (GI) tract of young kids remains largely unexplored. Therefore, we investigated the effects of doe roughage sources (alfalfa hay, AH, or corn straw, CS) during pregnancy and lactation on kid growth, GI morphology, barrier function, metabolism, immunity, and microbiome composition. The results indicate that, compared with the CS group, does fed an AH diet had significantly higher feed intake (p < 0.01). However, CS-fed does exhibited higher neutral detergent fiber (NDF) digestibility (p < 0.05). There were no significant differences in animal (doe or kid) weight among the groups (p > 0.05). In the rumen of goat kids, the AH group exhibited a higher papillae width and increased levels of interleukin-10 (IL-10) compared with the CS group (p < 0.05). In the jejunum of goat kids, the AH group showed a higher villus-height-to-crypt-depth (VH/CD) ratio, as well as elevated levels of secretory immunoglobulin A (SIgA), immunoglobulin G (IgG), IL-10, acetate, and total volatile fatty acids (TVFAs), when compared with the CS group (p < 0.05). Transcriptome analysis revealed that the source of roughage in does was associated with changes in the GI transcriptome of the kids. Differentially expressed genes (DEGs) in the rumen were mainly associated with tissue development and immune regulation, while the DEGs in the jejunum were mainly associated with the regulation of transferase activity. Spearman correlation analyses indicated significant associations between GI DEGs and phenotypic indicators related to GI development, immunity, and metabolism. LEfSe analysis identified 14 rumen microbial biomarkers and 6 jejunum microbial biomarkers. Notably, these microorganisms were also enriched in the rumen or day 28 milk of the does. Further microbial composition analysis revealed significant correlations between the rumen and milk microbiomes of does and the rumen or jejunum microbiomes of kids. Association analyses indicated that microbial biomarkers interact with host genes, thereby affecting the development and function of the GI system. Additionally, correlation analyses revealed significant association between milk metabolites and the rumen and jejunum microbiomes of kids. This study demonstrated that maternal diet significantly influences the development of microbial ecosystems in offspring by modulating microbial communities and metabolite composition. The early colonization of GI microorganisms is crucial for the structural development, barrier function, immune capacity, and microbial metabolic activity of the GI system.
Collapse
Affiliation(s)
- Haidong Du
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.D.); (W.G.); (M.N.); (J.Z.)
| | - Kenan Li
- Grassland Research Institute of Chinese Academy of Agricultural Sciences, Hohhot 010010, China;
| | - Wenliang Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.D.); (W.G.); (M.N.); (J.Z.)
| | - Meila Na
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.D.); (W.G.); (M.N.); (J.Z.)
| | - Jing Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.D.); (W.G.); (M.N.); (J.Z.)
| | - Renhua Na
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.D.); (W.G.); (M.N.); (J.Z.)
| |
Collapse
|
3
|
Reuben RC, Torres C. Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications. World J Microbiol Biotechnol 2025; 41:41. [PMID: 39826029 PMCID: PMC11742929 DOI: 10.1007/s11274-024-04242-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 12/26/2024] [Indexed: 01/20/2025]
Abstract
Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis. While single omics studies have undoubtedly contributed to our current understanding of milk microbiome and mastitis, they often provide limited information, targeting only a single biological viewpoint which is insufficient to provide system-wide information necessary for elucidating the biological footprints and molecular mechanisms driving mastitis and milk microbiome dysbiosis. Therefore, integrating a multi-omics approach in milk microbiome research could generate new knowledge, improve the current understanding of the functional and structural signatures of the milk ecosystem, and provide insights for sustainable mastitis control and microbiome management.
Collapse
Affiliation(s)
- Rine Christopher Reuben
- Biology Department, King's College, 133 North River Street, Wilkes-Barre, PA, 18711, USA.
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| |
Collapse
|
4
|
Urrutia-Angulo L, Ocejo M, Oporto B, Aduriz G, Lavín JL, Hurtado A. Unravelling the complexity of bovine milk microbiome: insights into mastitis through enterotyping using full-length 16S-metabarcoding. Anim Microbiome 2024; 6:58. [PMID: 39438939 PMCID: PMC11515664 DOI: 10.1186/s42523-024-00345-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 10/10/2024] [Indexed: 10/25/2024] Open
Abstract
BACKGROUND Mastitis, inflammation of the mammary gland, is a major disease of dairy cattle and the main cause for antimicrobial use. Although mainly caused by bacterial infections, the aetiological agent often remains unidentified by conventional microbiological culture methods. The aim of this study was to test whether shifts in the bovine mammary gland microbiota can result in initiation or progression of mastitis. METHODS Oxford-Nanopore long-read sequencing was used to generate full-length 16S rRNA gene reads (16S-metabarcoding) to characterise the microbial population of milk from healthy and diseased udder of cows classified into five groups based on their mastitis history and parity. RESULTS Samples were classified into six enterotypes, each characterised by a marker genus and several differentially-abundant genera. Two enterotypes were exclusively composed of clinical mastitis samples and displayed a marked dysbiosis, with a single pathogenic genus predominating and displacing the endogenous bacterial population. Other mastitis samples (all subclinical and half of the clinical) clustered with those from healthy animals into three enterotypes, probably reflecting intermediate states between health and disease. After an episode of clinical mastitis, clinical recovery and microbiome reconstitution do not always occur in parallel, indicating that the clinical definition of the udder health status does not consistently reflect the microbial profile. CONCLUSIONS These results show that mastitis is a dynamic process in which the udder microbiota constantly changes, highlighting the complexity of defining a unique microbiota profile indicative of mastitis.
Collapse
Affiliation(s)
- Leire Urrutia-Angulo
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Medelin Ocejo
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Beatriz Oporto
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Gorka Aduriz
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - José Luís Lavín
- Applied Mathematics Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain.
| |
Collapse
|
5
|
Khan MZ, Chen W, Li M, Ren W, Huang B, Kou X, Ullah Q, Wei L, Wang T, Khan A, Zhang Z, Li L, Wang C. Is there sufficient evidence to support the health benefits of including donkey milk in the diet? Front Nutr 2024; 11:1404998. [PMID: 39385792 PMCID: PMC11462490 DOI: 10.3389/fnut.2024.1404998] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 09/11/2024] [Indexed: 10/12/2024] Open
Abstract
Donkey milk has attracted attention due to its distinctive nutritional composition and potential health advantages, particularly because of its whey protein content, which includes lysozyme, α-lactalbumin, lactoferrin, and β-lactoglobulin and vitamin C, among other components. These elements contribute to immunoregulatory, antimicrobial, antioxidant, and anti-inflammatory properties, positioning donkey milk as a possible therapeutic option. In addition, due to the low levels of caseins, the casein-to-whey protein ratio, and the β-lactoglobulin content in donkey milk, it presents an optimal alternative for infant formula for individuals with cow's milk allergies. Moreover, research into donkey milk's potential for cancer prevention, diabetes management, and as a treatment for various diseases is ongoing, thanks to its bioactive peptides and components. Nevertheless, challenges such as its low production yield and the not fully understood mechanisms behind its potential therapeutic role necessitate more thorough investigation. This review consolidates the existing knowledge on the therapeutic possibilities of donkey milk, emphasizing its importance for human health and the need for more detailed studies to confirm its health benefits.
Collapse
Affiliation(s)
- Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Wenting Chen
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Mengmeng Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Wei Ren
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Xiyan Kou
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Qudrat Ullah
- Department of Theriogenology, Faculty of Veterinary and Animal Sciences, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Punjab, Pakistan
| | - Lin Wei
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Tongtong Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Adnan Khan
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenwei Zhang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Liangliang Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| |
Collapse
|
6
|
Mondragon Portocarrero ADC, Lopez-Santamarina A, Lopez PR, Ortega ISI, Duman H, Karav S, Miranda JM. Substitutive Effects of Milk vs. Vegetable Milk on the Human Gut Microbiota and Implications for Human Health. Nutrients 2024; 16:3108. [PMID: 39339708 PMCID: PMC11435326 DOI: 10.3390/nu16183108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 09/12/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
Background: In the last two decades, the consumption of plant-based dairy substitutes in place of animal-based milk has increased in different geographic regions of the world. Dairy substitutes of vegetable origin have a quantitative composition of macronutrients such as animal milk, although the composition of carbohydrates, proteins and fats, as well as bioactive components, is completely different from that of animal milk. Many milk components have been shown to have relevant effects on the intestinal microbiota. Methods: Therefore, the aim of this review is to compare the effects obtained by previous works on the composition of the gut microbiota after the ingestion of animal milk and/or vegetable beverages. Results: In general, the results obtained in the included studies were very positive for animal milk intake. Thus, we found an increase in gut microbiota richness and diversity, increase in the production of short-chain fatty acids, and beneficial microbes such as Bifidobacterium, lactobacilli, Akkermansia, Lachnospiraceae or Blautia. In other cases, we found a significant decrease in potential harmful bacteria such as Proteobacteria, Erysipelotrichaceae, Desulfovibrionaceae or Clostridium perfingens after animal-origin milk intake. Vegetable beverages have also generally produced positive results in the gut microbiota such as the increase in the relative presence of lactobacilli, Bifidobacterium or Blautia. However, we also found some potential negative results, such as increases in the presence of potential pathogens such as Enterobacteriaceae, Salmonella and Fusobacterium. Conclusions: From the perspective of their effects on the intestinal microbiota, milks of animal origin appear to be more beneficial for human health than their vegetable substitutes. These different effects on the intestinal microbiota should be considered in those cases where the replacement of animal milks by vegetable substitutes is recommended.
Collapse
Affiliation(s)
- Alicia del Carmen Mondragon Portocarrero
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (A.d.C.M.P.); (A.L.-S.); (P.R.L.)
| | - Aroa Lopez-Santamarina
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (A.d.C.M.P.); (A.L.-S.); (P.R.L.)
| | - Patricia Regal Lopez
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (A.d.C.M.P.); (A.L.-S.); (P.R.L.)
| | - Israel Samuel Ibarra Ortega
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo km. 4.5, Pachuca 42076, Hidalgo, Mexico;
| | - Hatice Duman
- Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale 17000, Türkiye; (H.D.); (S.K.)
| | - Sercan Karav
- Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale 17000, Türkiye; (H.D.); (S.K.)
| | - Jose Manuel Miranda
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (A.d.C.M.P.); (A.L.-S.); (P.R.L.)
| |
Collapse
|
7
|
Piras C, De Fazio R, Di Francesco A, Oppedisano F, Spina AA, Cunsolo V, Roncada P, Cramer R, Britti D. Detection of Antimicrobial Proteins/Peptides and Bacterial Proteins Involved in Antimicrobial Resistance in Raw Cow's Milk from Different Breeds. Antibiotics (Basel) 2024; 13:838. [PMID: 39335011 PMCID: PMC11429332 DOI: 10.3390/antibiotics13090838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Proteins involved in antibiotic resistance (resistome) and with antimicrobial activity are present in biological specimens. This study aims to explore the presence and abundance of antimicrobial peptides (AMPs) and resistome proteins in bovine milk from diverse breeds and from intensive (Pezzata rossa, Bruna alpina, and Frisona) and non-intensive farming (Podolica breeds). Liquid atmospheric pressure matrix-assisted laser desorption/ionization (LAP-MALDI) mass spectrometry (MS) profiling, bottom-up proteomics, and metaproteomics were used to comprehensively analyze milk samples from various bovine breeds in order to identify and characterize AMPs and to investigate resistome proteins. LAP-MALDI MS coupled with linear discriminant analysis (LDA) machine learning was employed as a rapid classification method for Podolica milk recognition against the milk of other bovine species. The results of the LAP-MALDI MS analysis of milk coupled with the linear discriminant analysis (LDA) demonstrate the potential of distinguishing between Podolica and control milk samples based on MS profiles. The classification accuracy achieved in the training set is 86% while it reaches 98.4% in the test set. Bottom-up proteomics revealed approximately 220 quantified bovine proteins (identified using the Bos taurus database), with cathelicidins and annexins exhibiting higher abundance levels in control cows (intensive farming breeds). On the other hand, the metaproteomics analysis highlighted the diversity within the milk's microbial ecosystem with interesting results that may reflect the diverse environmental variables. The bottom-up proteomics data analysis using the Comprehensive Antibiotic Resistance Database (CARD) revealed beta-lactamases and tetracycline resistance proteins in both control and Podolica milk samples, with no relevant breed-specific differences observed.
Collapse
Affiliation(s)
- Cristian Piras
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy; (R.D.F.); (F.O.); (A.A.S.); (P.R.); (D.B.)
- Interdepartmental Center Veterinary Service for Human and Animal Health, University “Magna Graecia” of Catanzaro, CISVetSUA, 88100 Catanzaro, Italy
| | - Rosario De Fazio
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy; (R.D.F.); (F.O.); (A.A.S.); (P.R.); (D.B.)
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, 95125 Catania, Italy; (A.D.F.); (V.C.)
| | - Francesca Oppedisano
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy; (R.D.F.); (F.O.); (A.A.S.); (P.R.); (D.B.)
- Institute of Research for Food Safety & Health (IRC-FSH), Department of Health Sciences, University of Catanzaro Magna Græcia, 88100 Catanzaro, Italy
| | - Anna Antonella Spina
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy; (R.D.F.); (F.O.); (A.A.S.); (P.R.); (D.B.)
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, 95125 Catania, Italy; (A.D.F.); (V.C.)
| | - Paola Roncada
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy; (R.D.F.); (F.O.); (A.A.S.); (P.R.); (D.B.)
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, UK;
| | - Domenico Britti
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy; (R.D.F.); (F.O.); (A.A.S.); (P.R.); (D.B.)
- Interdepartmental Center Veterinary Service for Human and Animal Health, University “Magna Graecia” of Catanzaro, CISVetSUA, 88100 Catanzaro, Italy
| |
Collapse
|
8
|
Tsifintaris M, Sitmalidis M, Tokamani M, Anastasiadi C, Georganta M, Tsochantaridis I, Vlachakis D, Tsikouras P, Nikolettos N, Chrousos GP, Sandaltzopoulos R, Giannakakis A. Analysis of Human Milk Microbiota in Northern Greece by Comparative 16S rRNA Sequencing vs. Local Dairy Animals. Nutrients 2024; 16:2175. [PMID: 39064618 PMCID: PMC11280067 DOI: 10.3390/nu16142175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Milk is a biological fluid with a dynamic composition of micronutrients and bioactive molecules that serves as a vital nutrient source for infants. Milk composition is affected by multiple factors, including genetics, geographical location, environmental conditions, lactation phase, and maternal nutrition, and plays a key role in dictating its microbiome. This study addresses a less-explored aspect, comparing the microbial communities in human breast milk with those in mature milk from species that are used for milk consumption. Since mature animal milk is used as a supplement for both the infant (formula) and the child/adolescent, our main aim was to identify shared microbial communities in colostrum and mature human milk. Using 16S rRNA metagenomic sequencing, we focused on characterizing the milk microbiota in the Northern Greek population by identifying shared microbial communities across samples and comparing the relative abundance of prevalent genera. We analyzed ten human milk samples (from five mothers), with five collected three days postpartum (colostrum) and five collected thirty to forty days postpartum (mature milk) from corresponding mothers. To perform an interspecies comparison of human milk microbiota, we analyzed five goat and five bovine milk samples from a local dairy industry, collected fifty to seventy days after birth. Alpha diversity analysis indicated moderate diversity and stability in bovine milk, high richness in goat milk, and constrained diversity in breast milk. Beta diversity analysis revealed significant distinctions among mammalian species, emphasizing both presence/absence and abundance-based clustering. Despite noticeable differences, shared microbial components underscore fundamental aspects across all mammalian species, highlighting the presence of a core microbiota predominantly comprising the Proteobacteria, Firmicutes, and Actinobacteriota phyla. At the genus level, Acinetobacter, Gemella, and Sphingobium exhibit significant higher abundance in human milk compared to bovine and goat milk, while Pseudomonas and Atopostipes are more prevalent in animal milk. Our comparative analysis revealed differences and commonalities in the microbial communities of various mammalian milks and unraveled the existence of a common fundamental milk core microbiome. We thus revealed both species-specific and conserved microbial communities in human, bovine, and goat milk. The existence of a common core microbiome with conserved differences between colostrum and mature human milk underscores fundamental similarities in the microbiota of milk across mammalian species, which could offer valuable implications for optimizing the nutritional quality and safety of dairy products as well as supplements for infant health.
Collapse
Affiliation(s)
- Margaritis Tsifintaris
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| | - Michail Sitmalidis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| | - Maria Tokamani
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| | - Christina Anastasiadi
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| | - Maria Georganta
- Department of Obstetrics and Gynecology, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ilias Tsochantaridis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| | - Dimitrios Vlachakis
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Panagiotis Tsikouras
- Department of Obstetrics and Gynecology, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Nikolaos Nikolettos
- Department of Obstetrics and Gynecology, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
- UNESCO Chair of Adolescent Health, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| | - Antonis Giannakakis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.)
| |
Collapse
|
9
|
Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR. The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk. mSystems 2024; 9:e0115823. [PMID: 38785438 PMCID: PMC11237780 DOI: 10.1128/msystems.01158-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
Collapse
Affiliation(s)
- C. J. Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Y. Deng
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. C. Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - F. Pena-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B. A. Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - S. M. Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L. S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N. R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
10
|
Linehan K, Patangia DV, Ross RP, Stanton C. Production, Composition and Nutritional Properties of Organic Milk: A Critical Review. Foods 2024; 13:550. [PMID: 38397527 PMCID: PMC10887702 DOI: 10.3390/foods13040550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/27/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Milk is one of the most valuable products in the food industry with most milk production throughout the world being carried out using conventional management, which includes intensive and traditional systems. The intensive use of fertilizers, antibiotics, pesticides and concerns regarding animal health and the environment have given increasing importance to organic dairy and dairy products in the last two decades. This review aims to compare the production, nutritional, and compositional properties of milk produced by conventional and organic dairy management systems. We also shed light on the health benefits of milk and the worldwide scenario of the organic dairy production system. Most reports suggest milk has beneficial health effects with very few, if any, adverse effects reported. Organic milk is reported to confer additional benefits due to its lower omega-6-omega-3 ratio, which is due to the difference in feeding practices, with organic cows predominantly pasture fed. Despite the testified animal, host, and environmental benefits, organic milk production is difficult in several regions due to the cost-intensive process and geographical conditions. Finally, we offer perspectives for a better future and highlight knowledge gaps in the organic dairy management system.
Collapse
Affiliation(s)
- Kevin Linehan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (K.L.); (D.V.P.)
- APC Microbiome Ireland, University College Cork, T12 Y120 Cork, Ireland;
- School of Microbiology, University College Cork, T12 XF62 Cork, Ireland
| | - Dhrati V. Patangia
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (K.L.); (D.V.P.)
- APC Microbiome Ireland, University College Cork, T12 Y120 Cork, Ireland;
- School of Microbiology, University College Cork, T12 XF62 Cork, Ireland
| | - Reynolds Paul Ross
- APC Microbiome Ireland, University College Cork, T12 Y120 Cork, Ireland;
- School of Microbiology, University College Cork, T12 XF62 Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (K.L.); (D.V.P.)
- APC Microbiome Ireland, University College Cork, T12 Y120 Cork, Ireland;
- VistaMilk Research Centre, Teagasc Moorepark, Fermoy, P61 C996 Cork, Ireland
| |
Collapse
|
11
|
Catassi G, Aloi M, Giorgio V, Gasbarrini A, Cammarota G, Ianiro G. The Role of Diet and Nutritional Interventions for the Infant Gut Microbiome. Nutrients 2024; 16:400. [PMID: 38337684 PMCID: PMC10857663 DOI: 10.3390/nu16030400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The infant gut microbiome plays a key role in the healthy development of the human organism and appears to be influenced by dietary practices through multiple pathways. First, maternal diet during pregnancy and infant nutrition significantly influence the infant gut microbiota. Moreover, breastfeeding fosters the proliferation of beneficial bacteria, while formula feeding increases microbial diversity. The timing of introducing solid foods also influences gut microbiota composition. In preterm infants the gut microbiota development is influenced by multiple factors, including the time since birth and the intake of breast milk, and interventions such as probiotics and prebiotics supplementation show promising results in reducing morbidity and mortality in this population. These findings underscore the need for future research to understand the long-term health impacts of these interventions and for further strategies to enrich the gut microbiome of formula-fed and preterm infants.
Collapse
Affiliation(s)
- Giulia Catassi
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Marina Aloi
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Valentina Giorgio
- Department of Woman and Child Health and Public Health, UOC Pediatria, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy;
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| |
Collapse
|