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Tu Z, Pang L, Lai S, Zhu Y, Wu Y, Zhou Q, Qi H, Zhang Y, Dong Y, Gan Y, Wu J, Yu J, Tao W, Ma B, Wang H, Zhang A. The hidden threat: Comprehensive assessment of antibiotic and disinfectant resistance in commercial pig slaughterhouses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174222. [PMID: 38945230 DOI: 10.1016/j.scitotenv.2024.174222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/08/2024] [Accepted: 06/21/2024] [Indexed: 07/02/2024]
Abstract
The presence of antibiotic resistance genes (ARGs), disinfectant resistance genes (DRGs), and pathogens in animal food processing environments (FAPE) poses a significant risk to human health. However, knowledge of the contamination and risk profiles of a typical commercial pig slaughterhouse with periodic disinfectant applications is limited. By creating the overall metagenomics-based behavior and risk profiles of ARGs, DRGs, and microbiomes in a nine-section pig slaughterhouse, an important FAPE in China. A total of 454 ARGs and 84 DRGs were detected in the slaughterhouse with resistance genes for aminoglycosides and quaternary ammonium compounds, respectively. The entire slaughtering chain is a hotspot for pathogens, including 83 human pathogenic bacteria (HPB), with 47 core HPB. In addition, 68 high-risk ARGs were significantly correlated with 55 HPB, 30 of which were recognized as potential bacteria co-resistant to antibiotics and disinfectants, confirm a three-fold risk of ARGs, DRGs, and pathogens prevailing throughout the chain. Pre-slaughter pig house (PSPH) was the major risk source for ARGs, DRGs, and HPB. Moreover, 75 Escherichia coli and 47 Proteus mirabilis isolates showed sensitivity to potassium monopersulfate and sodium hypochlorite, suggesting that slaughterhouses should use such related disinfectants. By using whole genome multi-locus sequence typing and single nucleotide polymorphism analyses, genetically closely related bacteria were identified across distinct slaughter sections, suggesting bacterial transmission across the slaughter chain. Overall, this study underscores the critical role of the PSPH section as a major source of HPB, ARGs, and DRGs contamination in commercial pig slaughterhouses. Moreover, it highlights the importance of addressing clonal transmission and cross-contamination of antibiotic- and disinfectant-resistant bacteria within and between slaughter sections. These issues are primarily attributed to the microbial load carried by animals before slaughter, carcass handling, and content exposure during visceral treatment. Our findings provide valuable insights for One Health-oriented slaughterhouse management practices.
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Affiliation(s)
- Zunfang Tu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Microbiological Testing and Research Department, Sichuan Institute for Drug Control (Sichuan Testing Center of Medical Devices), Chengdu 611731, China
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Shanming Lai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yixiao Zhu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yingting Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Quan Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haoxuan Qi
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yanhang Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yongyi Dong
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yumeng Gan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jie Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Yu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Weilai Tao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Bingcun Ma
- Microbiological Testing and Research Department, Sichuan Institute for Drug Control (Sichuan Testing Center of Medical Devices), Chengdu 611731, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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Fernandes MA, Delgado L, Almeida AC. The impact of probiotics on antibiotic resistance in newborns: A systematic review. J Neonatal Perinatal Med 2024:NPM240008. [PMID: 39058454 DOI: 10.3233/npm-240008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
BACKGROUND AND OBJECTIVES Newborns, particularly premature ones, are vulnerable to bacterial infections and often receive antibiotics, disrupting their normal intestinal microbiota. Probiotics have multiple health benefits and are recommended for restoring balance, but caution is needed due to potential consequences, such as promoting antibiotic resistance. Therefore, this study aimed to conduct a systematic review to assess current knowledge regarding the impact of probiotics on antibiotic resistance in newborns. METHODS This systematic review is aligned with the PRISMA 2020 statement. The search involved three electronic databases (PubMed, Scopus, and Web of Science) and the keywords used were "newborn", "probiotic", and "antibiotic resistance". Titles/abstracts were independently analyzed, followed by full-text assessments. Data extraction and synthesis were conducted, assessing outcomes like antibiotic resistance gene and mobile gene elements quantity and quality, vancomycin resistant enterococci colonization, antibiotic-resistant bacteria colonization, and microbiota changes. It was only included randomized controlled trials and cohort studies focusing on human newborns. RESULTS In the study selection process, 1,970 articles were identified and six were included in this review. The results varied, with two studies suggesting a positive impact of probiotics on antibiotic resistance, one a negative impact, while three others found no significant impact. Microbiota changes were also addressed across four studies, where the findings included promotion of beneficial bacteria and reduction of potential pathogens. Bias risk was evaluated using Joanna Briggs Institute tools. CONCLUSION Our findings did not allow for clear conclusions to be drawn, due to the observed heterogeneity between studies, highlighting the need for further studies.
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Affiliation(s)
| | - Lucinda Delgado
- Department of Pediatrics, Hospital Senhora da Oliveira - Guimarães, Portugal
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Marbun KT, Sugata M, Purnomo JS, Dikson, Mudana SO, Jan TT, Jo J. Genomic Characterization and Safety Assessment of Bifidobacterium breve BS2-PB3 as Functional Food. J Microbiol Biotechnol 2024; 34:871-879. [PMID: 38494884 DOI: 10.4014/jmb.2311.11031] [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: 11/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 03/19/2024]
Abstract
Our group had isolated Bifidobacterium breve strain BS2-PB3 from human breast milk. In this study, we sequenced the whole genome of B. breve BS2-PB3, and with a focus on its safety profile, various probiotic characteristics (presence of antibiotic resistance genes, virulence factors, and mobile elements) were then determined through bioinformatic analyses. The antibiotic resistance profile of B. breve BS2-PB3 was also evaluated. The whole genome of B. breve BS2-PB3 consisted of 2,268,931 base pairs with a G-C content of 58.89% and 2,108 coding regions. The average nucleotide identity and whole-genome phylogenetic analyses supported the classification of B. breve BS2-PB3. According to our in silico assessment, B. breve BS2-PB3 possesses antioxidant and immunomodulation properties in addition to various genes related to the probiotic properties of heat, cold, and acid stress, bile tolerance, and adhesion. Antibiotic susceptibility was evaluated using the Kirby-Bauer disk-diffusion test, in which the minimum inhibitory concentrations for selected antibiotics were subsequently tested using the Epsilometer test. B. breve BS2-PB3 only exhibited selected resistance phenotypes, i.e., to mupirocin (minimum inhibitory concentration/MIC >1,024 μg/ml), sulfamethoxazole (MIC >1,024 μg/ml), and oxacillin (MIC >3 μg/ml). The resistance genes against those antibiotics, i.e., ileS, mupB, sul4, mecC and ramA, were detected within its genome as well. While no virulence factor was detected, four insertion sequences were identified within the genome but were located away from the identified antibiotic resistance genes. In conclusion, B. breve BS2-PB3 demonstrated a sufficient safety profile, making it a promising candidate for further development as a potential functional food.
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Affiliation(s)
- Kristin Talia Marbun
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Marcelia Sugata
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Jonathan Suciono Purnomo
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Dikson
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Samuel Owen Mudana
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Tan Tjie Jan
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Juandy Jo
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15811, Indonesia
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Heppner N, Reitmeier S, Heddes M, Merino MV, Schwartz L, Dietrich A, List M, Gigl M, Meng C, van der Veen DR, Schirmer M, Kleigrewe K, Omer H, Kiessling S, Haller D. Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula. Cell Host Microbe 2024; 32:573-587.e5. [PMID: 38569545 DOI: 10.1016/j.chom.2024.02.015] [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: 10/25/2023] [Revised: 01/13/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024]
Abstract
Microbiota assembly in the infant gut is influenced by diet. Breastfeeding and human breastmilk oligosaccharides promote the colonization of beneficial bifidobacteria. Infant formulas are supplemented with bifidobacteria or complex oligosaccharides, notably galacto-oligosaccharides (GOS), to mimic breast milk. To compare microbiota development across feeding modes, this randomized controlled intervention study (German Clinical Trial DRKS00012313) longitudinally sampled infant stool during the first year of life, revealing similar fecal bacterial communities between formula- and breast-fed infants (N = 210) but differences across age. Infant formula containing GOS sustained high levels of bifidobacteria compared with formula containing B. longum and B. breve or placebo. Metabolite and bacterial profiling revealed 24-h oscillations and circadian networks. Rhythmicity in bacterial diversity, specific taxa, and functional pathways increased with age and was strongest following breastfeeding and GOS supplementation. Circadian rhythms in dominant taxa were further maintained ex vivo in a chemostat model. Hence, microbiota rhythmicity develops early in life and is impacted by diet.
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Affiliation(s)
- Nina Heppner
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Sandra Reitmeier
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Marjolein Heddes
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Michael Vig Merino
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Leon Schwartz
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Alexander Dietrich
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Gigl
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Daan R van der Veen
- Faculty of Health and Biomedical Science, University of Surrey, 388 Stag Hill Campus, Guildford 17 GU27XH, UK
| | - Melanie Schirmer
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Hélène Omer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Silke Kiessling
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany; Faculty of Health and Biomedical Science, University of Surrey, 388 Stag Hill Campus, Guildford 17 GU27XH, UK
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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Xu X, Feng Q, Zhang T, Gao Y, Cheng Q, Zhang W, Wu Q, Xu K, Li Y, Nguyen N, Taft DH, Mills DA, Lemay DG, Zhu W, Mao S, Zhang A, Xu K, Liu J. Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. IMETA 2024; 3:e169. [PMID: 38882494 PMCID: PMC11170968 DOI: 10.1002/imt2.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R 2 = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.
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Affiliation(s)
- Xinming Xu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Department of Nutrition and Food Hygiene, School of Public Health, Institute of Nutrition Fudan University Shanghai China
| | - Qingying Feng
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Biological Engineering Division Massachusetts Institute of Technology (MIT) Cambridge Massachusetts USA
| | - Tao Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Yunlong Gao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qu Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wanqiu Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qinglong Wu
- Department of Pathology and Immunology Baylor College of Medicine Houston Texas USA
| | - Ke Xu
- Department of Statistics University of Chicago Chicago Illinois
| | - Yucan Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute Fudan University Shanghai China
| | - Nhu Nguyen
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - Diana H Taft
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - David A Mills
- Department of Food Science and Technology University of California, Davis Davis California USA
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science University of California, Davis Davis California USA
| | - Danielle G Lemay
- USDA ARS Western Human Nutrition Research Center Davis California USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences Sichuan University Chengdu China
| | - Kelin Xu
- Department of Biostatistics, Key Laboratory of Public Health Safety, NHC Key Laboratory of Health Technology Assessment, School of Public Health Fudan University Shanghai China
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
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Trivedi A, Teo E, Walker KS. Probiotics for the postoperative management of term neonates after gastrointestinal surgery. Cochrane Database Syst Rev 2024; 1:CD012265. [PMID: 38258877 PMCID: PMC10804440 DOI: 10.1002/14651858.cd012265.pub2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
BACKGROUND The intestinal microflora has an essential role in providing a barrier against colonisation of pathogens, facilitating important metabolic functions, stimulating the development of the immune system, and maintaining intestinal motility. Probiotics are live microorganisms that can be administered to supplement the gut flora. Neonates who have undergone gastrointestinal surgery are particularly susceptible to infectious complications in the postoperative period. This may be partly due to a disruption of the integrity of the gut and its intestinal microflora. There may be a role for probiotics in reducing the incidence of sepsis and improving intestinal motility, thus reducing morbidity and mortality and improving enteral feeding in neonates in the postoperative period. OBJECTIVES To evaluate the efficacy and safety of administering probiotics after gastrointestinal surgery for the postoperative management of neonates born from 35 weeks of gestation. SEARCH METHODS We searched CENTRAL, MEDLINE, Embase, and trial registries in August 2023. We checked reference lists of included studies and relevant systematic reviews for additional studies. SELECTION CRITERIA We included randomised controlled trials (RCTs) that investigated the postoperative administration of oral probiotics versus placebo or no treatment in neonates born from 35 weeks of gestation who had one or more gastrointestinal surgical procedures. We applied no restrictions regarding the type or dosage of probiotics or the duration of treatment. DATA COLLECTION AND ANALYSIS We used standard Cochrane methods, and we used GRADE to assess the certainty of evidence. MAIN RESULTS We identified one RCT that recruited 61 neonates with a gestational age of 35 weeks or more. All infants were admitted to a neonatal intensive care unit and had surgery for gastrointestinal pathologies. There may be little or no difference in proven sepsis (positive bacterial culture, local or systemic) between infants who receive probiotics compared with those who receive placebo (odds ratio (OR) 0.64, 95% confidence interval (CI) 0.16 to 2.55; 61 infants; low-certainty evidence). Probiotics compared to placebo may have little or no effect on time to full enteral feeds (mean difference (MD) 0.63 days, 95% CI -4.02 to 5.28; 61 infants; low-certainty evidence). There were no reported deaths prior to discharge from hospital in either study arm. Two weeks after supplementation, the infants who received probiotics had a substantially higher relative abundance of non-pathogenic intestinal microflora (Bifidobacteriaceae) than those who received placebo (MD 38.22, 95% CI 28.40 to 48.04; 39 infants; low-certainty evidence). AUTHORS' CONCLUSIONS This review provides low-certainty evidence from one small RCT that probiotics compared to placebo have little or no effect on the risk of proven sepsis (positive bacterial culture, local or systemic) or time to full-enteral feeds in neonates who have undergone gastrointestinal surgery. Probiotics may substantially increase the abundance of beneficial bacterial in the intestine of these neonates, but the clinical implications of this finding are unknown. There is a need for adequately powered RCTs to assess the role of probiotics in this population. We identified two ongoing studies. As neither reported the gestational age of prospective study participants, we are unsure if they will be eligible for inclusion in this review.
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Affiliation(s)
- Amit Trivedi
- Grace Centre for Newborn Intensive Care, The Children's Hospital at Westmead, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Edward Teo
- Emergency Department, Concord Repatriation General Hospital, Sydney, Australia
| | - Karen S Walker
- Neonatal intensive Care Unit, Royal Prince Alfred hospital, Sydney, Australia
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7
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Gao Y, Liu J, Fang Y, Xu X, Wang F, Tang Y, Yin D, Cookson AL, Zhu W, Mao S, Zhong R. Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables. Microbiol Res 2024; 278:127540. [PMID: 37976735 DOI: 10.1016/j.micres.2023.127540] [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: 10/09/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.
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Affiliation(s)
- Yunlong Gao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yi Fang
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xinming Xu
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200030, China; Department of Nutrition and Food Hygiene, School of Public Health, Institute of Nutrition, Fudan University, Shanghai 200030, China
| | - Fei Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Yin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Adrian L Cookson
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand; AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North 4410, New Zealand
| | - Weiyun Zhu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Rongzhen Zhong
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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8
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Nadimpalli ML, Rojas Salvatierra L, Chakraborty S, Swarthout JM, Cabrera LZ, Pickering AJ, Calderon M, Saito M, Gilman RH, Pajuelo MJ. Effects of breastfeeding on children's gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru. Gut Microbes 2024; 16:2309681. [PMID: 38300753 PMCID: PMC10841006 DOI: 10.1080/19490976.2024.2309681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.
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Affiliation(s)
- Maya L. Nadimpalli
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Luismarcelo Rojas Salvatierra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Lilia Z. Cabrera
- Asociación Benéfica Proyectos en Informática, Salud, Medicina, y Agricultura (PRISMA), Lima, Peru
| | - Amy J. Pickering
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Blum Center for Developing Economies, University of California, Berkeley, CA, USA
| | - Maritza Calderon
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Monica J. Pajuelo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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9
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Patangia DV, Grimaud G, Wang S, Ross RP, Stanton C. Influence of age, socioeconomic status, and location on the infant gut resistome across populations. Gut Microbes 2024; 16:2297837. [PMID: 38217470 PMCID: PMC10793692 DOI: 10.1080/19490976.2023.2297837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024] Open
Abstract
Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.
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Affiliation(s)
- Dhrati V. Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R. Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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Vasco KA, Carbonell S, Sloup RE, Bowcutt B, Colwell RR, Graubics K, Erskine R, Norby B, Ruegg PL, Zhang L, Manning SD. Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle. Anim Microbiome 2023; 5:56. [PMID: 37946266 PMCID: PMC10636827 DOI: 10.1186/s42523-023-00274-4] [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: 06/07/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Intramammary (IMM) ceftiofur treatment is commonly used in dairy farms to prevent mastitis, though its impact on the cattle gut microbiome and selection of antibiotic-resistant bacteria has not been elucidated. Herein, we enrolled 40 dairy (Holstein) cows at the end of the lactation phase for dry-cow therapy: 20 were treated with IMM ceftiofur (Spectramast®DC) and a non-antibiotic internal teat sealant (bismuth subnitrate) and 20 (controls) received only bismuth subnitrate. Fecal grab samples were collected before and after treatment (weeks 1, 2, 3, 5, 7, and 9) for bacterial quantification and metagenomic next-generation sequencing. RESULTS Overall, 90% and 24% of the 278 samples had Gram-negative bacteria with resistance to ampicillin and ceftiofur, respectively. Most of the cows treated with ceftiofur did not have an increase in the number of resistant bacteria; however, a subset (25%) shed higher levels of ceftiofur-resistant bacteria for up to 2 weeks post-treatment. At week 5, the antibiotic-treated cows had lower microbiota abundance and richness, whereas a greater abundance of genes encoding extended-spectrum β-lactamases (ESBLs), CfxA, ACI-1, and CMY, was observed at weeks 1, 5 and 9. Moreover, the contig and network analyses detected associations between β-lactam resistance genes and phages, mobile genetic elements, and specific genera. Commensal bacterial populations belonging to Bacteroidetes most commonly possessed ESBL genes followed by members of Enterobacteriaceae. CONCLUSION This study highlights variable, persistent effects of IMM ceftiofur treatment on the gut microbiome and resistome in dairy cattle. Antibiotic-treated cattle had an increased abundance of specific taxa and genes encoding ESBL production that persisted for 9 weeks. Fecal shedding of ESBL-producing Enterobacteriaceae, which was classified as a serious public health threat, varied across animals. Together, these findings highlight the need for additional studies aimed at identifying factors associated with shedding levels and the dissemination and persistence of antibiotic resistance determinants on dairy farms across geographic locations.
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Affiliation(s)
- Karla A Vasco
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA
| | - Samantha Carbonell
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA
| | - Rebekah E Sloup
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA
| | - Bailey Bowcutt
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA
| | - Rita R Colwell
- University of Maryland, Institute for Advanced Computer Studies, College Park, MD, 20742, USA
- Cosmos ID, Inc, Germantown, MD, 20874, USA
| | | | - Ronald Erskine
- Department of Large Animal Clinical Sciences, Michigan State University, E. Lansing, MI, 48824, USA
| | - Bo Norby
- Department of Large Animal Clinical Sciences, Michigan State University, E. Lansing, MI, 48824, USA
| | - Pamela L Ruegg
- Department of Large Animal Clinical Sciences, Michigan State University, E. Lansing, MI, 48824, USA.
| | - Lixin Zhang
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA.
- Department of Epidemiology and Biostatistics, Michigan State University, E. Lansing, MI, 48824, USA.
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA.
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11
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Gutierrez A, Pucket B, Engevik MA. Bifidobacterium and the intestinal mucus layer. MICROBIOME RESEARCH REPORTS 2023; 2:36. [PMID: 38045921 PMCID: PMC10688832 DOI: 10.20517/mrr.2023.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 12/05/2023]
Abstract
Bifidobacterium species are integral members of the human gut microbiota and these microbes have significant interactions with the intestinal mucus layer. This review delves into Bifidobacterium-mucus dynamics, shedding light on the multifaceted nature of this relationship. We cover conserved features of Bifidobacterium-mucus interactions, such as mucus adhesion and positive regulation of goblet cell and mucus production, as well as species and strain-specific attributes of mucus degradation. For each interface, we explore the molecular mechanisms underlying these interactions and their potential implications for human health. Notably, we emphasize the ability of Bifidobacterium species to positively influence the mucus layer, shedding light on its potential as a mucin-builder and a therapeutic agent for diseases associated with disrupted mucus barriers. By elucidating the complex interplay between Bifidobacterium and intestinal mucus, we aim to contribute to a deeper understanding of the gut microbiota-host interface and pave the way for novel therapeutic strategies.
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Affiliation(s)
- Alyssa Gutierrez
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Brenton Pucket
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Melinda A. Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
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12
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Melsaether C, Høtoft D, Wellejus A, Hermes GDA, Damholt A. Seeding the Infant Gut in Early Life-Effects of Maternal and Infant Seeding with Probiotics on Strain Transfer, Microbiota, and Gastrointestinal Symptoms in Healthy Breastfed Infants. Nutrients 2023; 15:4000. [PMID: 37764787 PMCID: PMC10538230 DOI: 10.3390/nu15184000] [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: 07/12/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
We investigated the effects of two dosing regimens of two multi-strain probiotic products on the gut microbiota of breastfed infants, including the transfer of the dosed strains and clinical outcomes. In forty-seven dyads, infants were either exposed through maternal intake (MS) of Lactobacillus acidophilus LA-5, Bifidobacterium animalis subsp. lactis BB-12, Lacticaseibacillus rhamnosus LGG, and Bifidobacterium longum subsp. infantis Bifin02 from gestational week thirty-three until four weeks after birth (n = 24) or dosed directly (IS) with the same strains except for LA-5 starting within 24 h after birth until day 28 (n = 23). Infant stool samples were collected on day 0, 14, 28, and 42 after birth. Gastrointestinal symptoms were assessed by parents using an electronic diary. Microbiota composition was determined using 16S rRNA sequencing, and strain recovery was analyzed by qPCR. Notably, 100% of the IS infants were colonized with Bifin02 after 14 days as opposed to only 25% of the MS infants. Mean stool frequency was significantly lower in IS infants compared to MS infants and IS infants had softer stools on day 14, 28, and 42. A significantly steeper slope of progression of inconsolable crying and fussing was observed in MS infants compared to IS infants. In conclusion, direct infant seeding induced a faster increase in fecal bifidobacteria abundancy and Bifin02 recovery compared to dosed through the maternal intake.
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Affiliation(s)
- Cathrine Melsaether
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
| | - Diana Høtoft
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark;
| | - Anja Wellejus
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
| | - Gerben D. A. Hermes
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
| | - Anders Damholt
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
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13
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Larke JA, Heiss BE, Ehrlich AM, Taft DH, Raybould HE, Mills DA, Slupsky CM. Milk oligosaccharide-driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice. MICROBIOME 2023; 11:194. [PMID: 37635250 PMCID: PMC10463478 DOI: 10.1186/s40168-023-01624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/14/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Bifidobacteria represent an important gut commensal in humans, particularly during initial microbiome assembly in the first year of life. Enrichment of Bifidobacterium is mediated though the utilization of human milk oligosaccharides (HMOs), as several human-adapted species have dedicated genomic loci for transport and metabolism of these glycans. This results in the release of fermentation products into the gut lumen which may offer physiological benefits to the host. Synbiotic pairing of probiotic species with a cognate prebiotic delivers a competitive advantage, as the prebiotic provides a nutrient niche. METHODS To determine the fitness advantage and metabolic characteristics of an HMO-catabolizing Bifidobacterium strain in the presence or absence of 2'-fucosyllactose (2'-FL), conventionally colonized mice were gavaged with either Bifidobacterium pseudocatenulatum MP80 (B.p. MP80) (as the probiotic) or saline during the first 3 days of the experiment and received water or water containing 2'-FL (as the prebiotic) throughout the study. RESULTS 16S rRNA gene sequencing revealed that mice provided only B.p. MP80 were observed to have a similar microbiota composition as control mice throughout the experiment with a consistently low proportion of Bifidobacteriaceae present. Using 1H NMR spectroscopy, similar metabolic profiles of gut luminal contents and serum were observed between the control and B.p. MP80 group. Conversely, synbiotic supplemented mice exhibited dramatic shifts in their community structure across time with an overall increased, yet variable, proportion of Bifidobacteriaceae following oral inoculation. Parsing the synbiotic group into high and moderate bifidobacterial persistence based on the median proportion of Bifidobacteriaceae, significant differences in gut microbial diversity and metabolite profiles were observed. Notably, metabolites associated with the fermentation of 2'-FL by bifidobacteria were significantly greater in mice with a high proportion of Bifidobacteriaceae in the gut suggesting metabolite production scales with population density. Moreover, 1,2-propanediol, a fucose fermentation product, was only observed in the liver and brain of mice harboring high proportions of Bifidobacteriaceae. CONCLUSIONS This study reinforces that the colonization of the gut with a commensal microorganism does not guarantee a specific functional output. Video Abstract.
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Affiliation(s)
- Jules A Larke
- Department of Nutrition, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Britta E Heiss
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Amy M Ehrlich
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, , Davis, CA, USA
| | - Diana H Taft
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Helen E Raybould
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, , Davis, CA, USA
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
| | - Carolyn M Slupsky
- Department of Nutrition, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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14
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Theophilus RJ, Taft DH. Antimicrobial Resistance Genes (ARGs), the Gut Microbiome, and Infant Nutrition. Nutrients 2023; 15:3177. [PMID: 37513595 PMCID: PMC10383493 DOI: 10.3390/nu15143177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The spread of antimicrobial resistance genes (ARGs) is a major public health crisis, with the ongoing spread of ARGs leading to reduced efficacy of antibiotic treatments. The gut microbiome is a key reservoir for ARGs, and because diet shapes the gut microbiome, diet also has the potential to shape the resistome. This diet-gut microbiome-resistome relationship may also be important in infants and young children. This narrative review examines what is known about the interaction between the infant gut microbiome, the infant resistome, and infant nutrition, including exploring the potential of diet to mitigate infant ARG carriage. While more research is needed, diet has the potential to reduce infant and toddler carriage of ARGs, an important goal as part of maintaining the efficacy of available antibiotics and preserving infant and toddler health.
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Affiliation(s)
- Rufus J Theophilus
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Diana Hazard Taft
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
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15
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Leo S, Cetiner OF, Pittet LF, Messina NL, Jakob W, Falquet L, Curtis N, Zimmermann P. Metagenomics analysis of the neonatal intestinal resistome. Front Pediatr 2023; 11:1169651. [PMID: 37397142 PMCID: PMC10313230 DOI: 10.3389/fped.2023.1169651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/25/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome. Objective The objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates. Methods Shotgun metagenomics was used to analyse the resistome in stool samples collected at 1 week of age from 390 healthy, term-born neonates who did not receive antibiotics. Results Overall, 913 ARGs belonging to 27 classes were identified. The most abundant ARGs were those conferring resistance to tetracyclines, quaternary ammonium compounds, and macrolide-lincosamide-streptogramin-B. Phylogenetic composition was strongly associated with the resistome composition. Other factors that were associated with the abundance of ARGs were delivery mode, gestational age, birth weight, feeding method, and antibiotics in the last trimester of pregnancy. Sex, ethnicity, probiotic use during pregnancy, and intrapartum antibiotics had little effect on the abundance of ARGs. Conclusion Even in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs.
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Affiliation(s)
- Stefano Leo
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
| | - Omer F. Cetiner
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Laure F. Pittet
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicole L. Messina
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - William Jakob
- Microbiology Laboratory, Fribourg Hospital, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
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16
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The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705. Microorganisms 2023; 11:microorganisms11030588. [PMID: 36985162 PMCID: PMC10059941 DOI: 10.3390/microorganisms11030588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Bifidobacteria are saccharolytic bacteria that are able to metabolize a relatively large range of carbohydrates through their unique central carbon metabolism known as the “bifid-shunt”. Carbohydrates have been shown to modulate the growth rate of bifidobacteria, but unlike for other genera (e.g., E. coli or L. lactis), the impact it may have on the overall physiology of the bacteria has not been studied in detail to date. Using glucose and galactose as model substrates in Bifidobacterium longum NCC 2705, we established that the strain displayed fast and slow growth rates on those carbohydrates, respectively. We show that these differential growth conditions are accompanied by global transcriptional changes and adjustments of central carbon fluxes. In addition, when grown on galactose, NCC 2705 cells were significantly smaller, exhibited an expanded capacity to import and metabolized different sugars and displayed an increased acid-stress resistance, a phenotypic signature associated with generalized fitness. We predict that part of the observed adaptation is regulated by the previously described bifidobacterial global transcriptional regulator AraQ, which we propose to reflect a catabolite-repression-like response in B. longum. With this manuscript, we demonstrate that not only growth rate but also various physiological characteristics of B. longum NCC 2705 are responsive to the carbon source used for growth, which is relevant in the context of its lifestyle in the human infant gut where galactose-containing oligosaccharides are prominent.
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17
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Ruiz-Ojeda FJ, Plaza-Diaz J, Morales J, Álvarez-Calatayud G, Climent E, Silva Á, Martinez-Blanch JF, Enrique M, Tortajada M, Ramon D, Alvarez B, Chenoll E, Gil Á. Effects of a Novel Infant Formula on the Fecal Microbiota in the First Six Months of Life: The INNOVA 2020 Study. Int J Mol Sci 2023; 24:3034. [PMID: 36769356 PMCID: PMC9917896 DOI: 10.3390/ijms24033034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Exclusive breastfeeding is highly recommended for infants for at least the first six months of life. However, for some mothers, it may be difficult or even impossible to do so. This can lead to disturbances in the gut microbiota, which in turn may be related to a higher incidence of acute infectious diseases. Here, we aimed to evaluate whether a novel starting formula versus a standard formula provides a gut microbiota composition more similar to that of breastfed infants in the first 6 months of life. Two hundred and ten infants (70/group) were enrolled in the study and completed the intervention until 12 months of age. For the intervention period, infants were divided into three groups: Group 1 received formula 1 (INN) with a lower amount of protein, a proportion of casein to whey protein ratio of about 70/30 by increasing the content of α-lactalbumin, and with double the amount of docosahexaenoic acid/arachidonic acid than the standard formula; INN also contained a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis). Group 2 received the standard formula (STD) and the third group was exclusively breastfed (BF) for exploratory analysis. During the study, visits were made at 21 days, 2, 4, and 6 months of age, with ±3 days for the visit at 21 days of age, ±1 week for the visit at 2 months, and ±2 weeks for the others. Here, we reveal how consuming the INN formula promotes a similar gut microbiota composition to those infants that were breastfed in terms of richness and diversity, genera, such as Bacteroides, Bifidobacterium, Clostridium, and Lactobacillus, and calprotectin and short-chain fatty acid levels at 21 days, 2 and 6 months. Furthermore, we observed that the major bacteria metabolic pathways were more alike between the INN formula and BF groups compared to the STD formula group. Therefore, we assume that consumption of the novel INN formula might improve gut microbiota composition, promoting a healthier intestinal microbiota more similar to that of an infant who receives exclusively human milk.
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Affiliation(s)
- Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Neuherberg, 85764 Munich, Germany
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Armilla, Spain
| | - Julio Plaza-Diaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Javier Morales
- Product Development Department, Alter Farmacia SA, 28880 Madrid, Spain
| | | | - Eric Climent
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Ángela Silva
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | | | - María Enrique
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Marta Tortajada
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Daniel Ramon
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Beatriz Alvarez
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Empar Chenoll
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Armilla, Spain
- CIBEROBN, CIBER Physiopathology of Obesity and Nutrition, Instituto de Salud Carlos III, 28029 Madrid, Spain
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18
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Larke JA, Bacalzo N, Castillo JJ, Couture G, Chen Y, Xue Z, Alkan Z, Kable ME, Lebrilla CB, Stephensen CB, Lemay DG. Dietary Intake of Monosaccharides from Foods is Associated with Characteristics of the Gut Microbiota and Gastrointestinal Inflammation in Healthy US Adults. J Nutr 2023; 153:106-119. [PMID: 36913444 PMCID: PMC10196574 DOI: 10.1016/j.tjnut.2022.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/15/2022] [Accepted: 12/14/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Current assessment of dietary carbohydrates does not adequately reflect the nutritional properties and effects on gut microbial structure and function. Deeper characterization of food carbohydrate composition can serve to strengthen the link between diet and gastrointestinal health outcomes. OBJECTIVES The present study aims to characterize the monosaccharide composition of diets in a healthy US adult cohort and use these features to assess the relationship between monosaccharide intake, diet quality, characteristics of the gut microbiota, and gastrointestinal inflammation. METHODS This observational, cross-sectional study enrolled males and females across age (18-33 y, 34-49 y, and 50-65 y) and body mass index (normal, 18.5-24.99 kg/m2; overweight, 25-29.99 kg/m2; and obese, 30-44 kg/m2) categories. Recent dietary intake was assessed by the automated self-administered 24-h dietary recall system, and gut microbiota were assessed with shotgun metagenome sequencing. Dietary recalls were mapped to the Davis Food Glycopedia to estimate monosaccharide intake. Participants with >75% of carbohydrate intake mappable to the glycopedia were included (N = 180). RESULTS Diversity of monosaccharide intake was positively associated with the total Healthy Eating Index score (Pearson's r = 0.520, P = 1.2 × 10-13) and negatively associated with fecal neopterin (Pearson's r = -0.247, P = 3.0 × 10-3). Comparing high with low intake of specific monosaccharides revealed differentially abundant taxa (Wald test, P < 0.05), which was associated with the functional capacity to break down these monomers (Wilcoxon rank-sum test, P < 0.05). CONCLUSIONS Monosaccharide intake was associated with diet quality, gut microbial diversity, microbial metabolism, and gastrointestinal inflammation in healthy adults. As specific food sources were rich in particular monosaccharides, it may be possible in the future to tailor diets to fine-tune the gut microbiota and gastrointestinal function. This trial is registered at www. CLINICALTRIALS gov as NCT02367287.
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Affiliation(s)
- Jules A Larke
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA
| | - Nikita Bacalzo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Zhengyao Xue
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA; Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Zeynep Alkan
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA
| | - Mary E Kable
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA; Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA; Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Charles B Stephensen
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA; Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Danielle G Lemay
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA; Department of Nutrition, University of California, Davis, Davis, CA, USA.
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19
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Mills DA, German JB, Lebrilla CB, Underwood MA. Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants. Gut Microbes 2023; 15:2192458. [PMID: 37013357 PMCID: PMC10075334 DOI: 10.1080/19490976.2023.2192458] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
For over a century, physicians have witnessed a common enrichment of bifidobacteria in the feces of breast-fed infants that was readily associated with infant health status. Recent advances in bacterial genomics, metagenomics, and glycomics have helped explain the nature of this unique enrichment and enabled the tailored use of probiotic supplementation to restore missing bifidobacterial functions in at-risk infants. This review documents a 20-year span of discoveries that set the stage for the current use of human milk oligosaccharide-consuming bifidobacteria to beneficially colonize, modulate, and protect the intestines of at-risk, human milk-fed, neonates. This review also presents a model for probiotic applications wherein bifidobacterial functions, in the form of colonization and HMO-related catabolic activity in situ, represent measurable metabolic outcomes by which probiotic efficacy can be scored toward improving infant health.
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Affiliation(s)
- David A. Mills
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Department of Viticulture and Enology, University of California-Davis, Davis, CA, United States
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
| | - J. Bruce German
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
- Department of Chemistry, University of California-Davis, Davis, CA, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, CA, United States
| | - Mark A. Underwood
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
- Division of Neonatology, Department of Pediatrics, University of California-Davis, Sacramento, CA, United States
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20
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Mullaney JA, Roy NC, Halliday C, Young W, Altermann E, Kruger MC, Dilger RN, McNabb WC. Effects of early postnatal life nutritional interventions on immune-microbiome interactions in the gastrointestinal tract and implications for brain development and function. Front Microbiol 2022; 13:960492. [PMID: 36504799 PMCID: PMC9726769 DOI: 10.3389/fmicb.2022.960492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
The gastrointestinal (GI) microbiota has co-evolved with the host in an intricate relationship for mutual benefit, however, inappropriate development of this relationship can have detrimental effects. The developing GI microbiota plays a vital role during the first 1,000 days of postnatal life, during which occurs parallel development and maturation of the GI tract, immune system, and brain. Several factors such as mode of delivery, gestational age at birth, exposure to antibiotics, host genetics, and nutrition affect the establishment and resultant composition of the GI microbiota, and therefore play a role in shaping host development. Nutrition during the first 1,000 days is considered to have the most potential in shaping microbiota structure and function, influencing its interactions with the immune system in the GI tract and consequent impact on brain development. The importance of the microbiota-GI-brain (MGB) axis is also increasingly recognized for its importance in these developmental changes. This narrative review focuses on the importance of the GI microbiota and the impact of nutrition on MGB axis during the immune system and brain developmental period in early postnatal life of infants.
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Affiliation(s)
- Jane A. Mullaney
- Riddet Institute, Massey University, Palmerston North, New Zealand,AgResearch, Palmerston North, New Zealand,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C. Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand,High-Value Nutrition National Science Challenge, Auckland, New Zealand,Department of Human Nutrition, University of Otago, Dunedin, New Zealand
| | - Christine Halliday
- Riddet Institute, Massey University, Palmerston North, New Zealand,AgResearch, Palmerston North, New Zealand,School of Food and Advanced Technology, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Wayne Young
- Riddet Institute, Massey University, Palmerston North, New Zealand,AgResearch, Palmerston North, New Zealand,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Eric Altermann
- Riddet Institute, Massey University, Palmerston North, New Zealand,High-Value Nutrition National Science Challenge, Auckland, New Zealand,School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Marlena C. Kruger
- School of Health Sciences, College of Health, Massey University, Palmerston North, New Zealand
| | - Ryan N. Dilger
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Warren C. McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand,High-Value Nutrition National Science Challenge, Auckland, New Zealand,*Correspondence: Warren C. McNabb,
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21
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Ko YJ, Kim S, Pan CH, Park K. Identification of Functional Microbial Modules Through Network-Based Analysis of Meta-Microbial Features Using Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2851-2862. [PMID: 34329170 DOI: 10.1109/tcbb.2021.3100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As the microbiome is composed of a variety of microbial interactions, it is imperative in microbiome research to identify a microbial sub-community that collectively conducts a specific function. However, current methodologies have been highly limited to analyzing conditional abundance changes of individual microorganisms without considering group-wise collective microbial features. To overcome this limitation, we developed a network-based method using nonnegative matrix factorization (NMF) to identify functional meta-microbial features (MMFs) that, as a group, better discriminate specific environmental conditions of samples using microbiome data. As proof of concept, large-scale human microbiome data collected from different body sites were used to identify body site-specific MMFs by applying NMF. The statistical test for MMFs led us to identify highly discriminative MMFs on sample classes, called synergistic MMFs (SYMMFs). Finally, we constructed a SYMMF-based microbial interaction network (SYMMF-net) by integrating all of the SYMMF information. Network analysis revealed core microbial modules closely related to critical sample properties. Similar results were also found when the method was applied to various disease-associated microbiome data. The developed method interprets high-dimensional microbiome data by identifying functional microbial modules on sample properties and intuitively representing their systematic relationships via a microbial network.
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22
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Guitor AK, Yousuf EI, Raphenya AR, Hutton EK, Morrison KM, McArthur AG, Wright GD, Stearns JC. Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. MICROBIOME 2022; 10:136. [PMID: 36008821 PMCID: PMC9414150 DOI: 10.1186/s40168-022-01327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. RESULTS At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. CONCLUSIONS This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.
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Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Jennifer C Stearns
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada.
- Department of Medicine, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
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23
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Leo S, Curtis N, Zimmermann P. The neonatal intestinal resistome and factors that influence it - a systematic review. Clin Microbiol Infect 2022; 28:1539-1546. [PMID: 35868586 DOI: 10.1016/j.cmi.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The intestinal microbiome provides a reservoir for antibiotic resistance genes (ARGs). The neonatal microbiome is more susceptible to disturbance from external factors than the established microbiome. OBJECTIVES In this review, we systematically summarise studies which investigated the intestinal resistome in neonates. DATA SOURCES MEDLINE and Embase databases were searched. STUDY ELIGIBILITY CRITERIA We included original studies which investigated ARGs in stool or rectal swabs in neonates using molecular diagnostics. METHODS OF DATA SYNTHESIS Two authors independently extracted data. Data was summarised in tables. RESULTS Our search identified 2,701 studies, of which 23 (22 cohorts) were included. The studies show that the neonatal intestine harbours a high abundance and variety of ARGs, even in the absence of direct antibiotic exposure. The most-commonly found ARGs confer resistance to aminoglycosides, beta-lactams, macrolides, tetracyclines or multi-drug resistance. There is evidence that ARGs can be transferred from mothers to neonates. Interestingly, however, compared to mothers, neonates are reported to have a higher abundance of ARGs. One likely reason for this is the bacterial phylogenetic composition with a high abundance of Gammaproteobacteria in neonatal stool. Factors that have been associated with a higher abundance of ARGs are intrapartum and neonatal antibiotic use. Breastfeeding and neonatal probiotic use have been associated with a lower abundance of ARGs. Antibiotics during pregnancy, delivery mode or sex are reported to have little effect. However, this might be because studies were underpowered and because it is difficult to account for effect modifiers. DISCUSSION The neonatal intestine seems to have a lower colonisation resistance, which could make it easier for antibiotic-resistant populations to establish themselves. Future studies will help in the development of evidence-based interventions to modulate the abundance of ARGs in neonates, for example, by the use of pre- and probiotics and bacteriophages.
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Affiliation(s)
- Stefano Leo
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
| | - Nigel Curtis
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
| | - Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland; Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia.
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24
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German JB, Lebrilla C, Mills DA. Milk: A Scientific Model for Diet and Health Research in the 21st Century. Front Nutr 2022; 9:922907. [PMID: 35757260 PMCID: PMC9226620 DOI: 10.3389/fnut.2022.922907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
The origin of lactation and the composition, structures and functions of milk's biopolymers highlight the Darwinian pressure on lactation as a complete, nourishing and protective diet. Lactation, under the driving pressure to be a sustainable bioreactor, was under selection pressure of its biopolymers with diverse functions acting from the mammary gland through the digestive system of the infant. For example, milk is extensively glycosylated and the glycan structures and their functions are now emerging. Milk contains free oligosaccharides; complex polymers of sugars whose stereospecific linkages are not matched by glycosidic enzymes within the mammalian infant gut. These glycan polymers reach the lower intestine undigested. In this microbe-rich environment, bacteria compete to release and ferment the sugars via different hydrolytic strategies. One specific type of bacteria, Bifidobacterium longum subsp. infantis, (B. infantis) is uniquely equipped with a repertoire of genes encoding enzymes capable of taking up, hydrolyzing and metabolizing the complex glycans of human milk. This combination of a distinct food supply and unique genetic capability shapes the composition and metabolic products of the entire microbial community within the lower intestine of breast fed infants. The intestinal microbiome dominated by B. infantis, shields the infant from the growth of gram negative enteropathogens and their endotoxins as a clear health benefit. The world is facing unprecedented challenges to produce a food supply that is both nourishing, safe and sustainable. Scientists need to guide the future of agriculture and food in response to these 21st century challenges. Lactation provides an inspiring model of what that future research strategy could be.
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Affiliation(s)
- J Bruce German
- University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Davis, CA, United States.,Foods for Health Institute, Davis, CA, United States
| | - Carlito Lebrilla
- University of California, Davis, Davis, CA, United States.,Department of Chemistry, Davis, CA, United States
| | - David A Mills
- University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Davis, CA, United States.,Foods for Health Institute, Davis, CA, United States
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25
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Duboux S, Muller JA, De Franceschi F, Mercenier A, Kleerebezem M. Using fluorescent promoter-reporters to study sugar utilization control in Bifidobacterium longum NCC 2705. Sci Rep 2022; 12:10477. [PMID: 35729224 PMCID: PMC9213400 DOI: 10.1038/s41598-022-14638-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
Bifidobacteria are amongst the first bacteria to colonize the human gastro-intestinal system and have been proposed to play a crucial role in the development of the infant gut since their absence is correlated to the development of diseases later in life. Bifidobacteria have the capacity to metabolize a diverse range of (complex) carbohydrates, reflecting their adaptation to the lower gastro-intestinal tract. Detailed understanding of carbohydrate metabolism regulation in this genus is of prime importance and availability of additional genetic tools easing such studies would be beneficial. To develop a fluorescent protein-based reporter system that can be used in B. longum NCC 2705, we first selected the most promising fluorescent protein out of the seven we tested (i.e., mCherry). This reporter protein was then used to study the carbohydrate mediated activation of PBl1518 and PBl1694, two promoters respectively predicted to be controlled by the transcriptional factors AraQ and AraU, previously suggested to regulate arabinose utilization and proposed to also act as global transcriptional regulators in bifidobacteria. We confirmed that in B. longum NCC 2705 the AraQ controlled promoter (PBl1518) is induced strongly by arabinose and established that the AraU controlled promoter (PBl1694) was mostly induced by the hexoses galactose and fructose. Combining the mCherry reporter system with flow cytometry, we established that NCC 2705 is able to co-metabolize arabinose and glucose while galactose was only consumed after glucose exhaustion, thus illustrating the complexity of different carbohydrate consumption patterns and their specific regulation in this strain.
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Affiliation(s)
- S Duboux
- Nestlé Research, Lausanne, Switzerland. .,Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
| | | | | | - A Mercenier
- Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands
| | - M Kleerebezem
- Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
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Abstract
Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24®] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR. IMPORTANCE Antimicrobial resistance (AMR) represents a considerable burden to health care systems, with the public health community largely in consensus that AMR will be a major cause of death worldwide in the coming decades. Humans carry antibiotic resistance in the microbes that live in and on us, collectively known as the human microbiome. Diet is a powerful method for shaping the human gut microbiome and may be a tractable method for lessening antibiotic resistance, and yet little is known about the relationship between diet and AMR. We examined this relationship in healthy individuals who contained various abundances of antibiotic resistance genes and found that individuals who consumed diverse diets that were high in fiber and low in animal protein had fewer antibiotic resistance genes. Dietary interventions may be useful for lessening the burden of antimicrobial resistance and might ultimately motivate dietary guidelines which will consider how nutrition can reduce the impact of infectious disease.
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Oladeinde A, Abdo Z, Zwirzitz B, Woyda R, Lakin SM, Press MO, Cox NA, Thomas JC, Looft T, Rothrock MJ, Zock G, Plumblee Lawrence J, Cudnik D, Ritz C, Aggrey SE, Liachko I, Grove JR, Wiersma C. Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens. Appl Environ Microbiol 2022; 88:e0251721. [PMID: 35416680 PMCID: PMC9107613 DOI: 10.1128/aem.02517-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/06/2022] [Indexed: 12/15/2022] Open
Abstract
Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.
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Affiliation(s)
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | - Benjamin Zwirzitz
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | - Steven M Lakin
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | | | - Nelson A Cox
- U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
| | - Jesse C Thomas
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Torey Looft
- National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | | | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | | | - Denice Cudnik
- U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
| | - Casey Ritz
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | | | | | - Crystal Wiersma
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
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28
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Lorenzo PM, Izquierdo AG, Rodriguez-Carnero G, Fernández-Pombo A, Iglesias A, Carreira MC, Tejera C, Bellido D, Martinez-Olmos MA, Leis R, Casanueva FF, Crujeiras AB. Epigenetic Effects of Healthy Foods and Lifestyle Habits from the Southern European Atlantic Diet Pattern: A Narrative Review. Adv Nutr 2022; 13:1725-1747. [PMID: 35421213 PMCID: PMC9526853 DOI: 10.1093/advances/nmac038] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/21/2022] [Indexed: 01/28/2023] Open
Abstract
Recent scientific evidence has shown the importance of diet and lifestyle habits for the proper functioning of the human body. A balanced and healthy diet, physical activity, and psychological well-being have a direct beneficial effect on health and can have a crucial role in the development and prognosis of certain diseases. The Southern European Atlantic diet, also named the Atlantic diet, is a unique dietary pattern that occurs in regions that present higher life expectancy, suggesting that this specific dietary pattern is associated with positive health effects. In fact, it is enriched with nutrients of high biological value, which, together with its cooking methods, physical activity promotion, reduction in carbon footprint, and promoting of family meals, promote these positive effects on health. The latest scientific advances in the field of nutri-epigenetics have revealed that epigenetic markers associated with food or nutrients and environmental factors modulate gene expression and, therefore, are involved with both health and disease. Thus, in this review, we evaluated the main aspects that define the Southern European Atlantic diet and the potential epigenetic changes associated with them based on recent studies regarding the main components of these dietary patterns. In conclusion, based on the information existing in the literature, we postulate that the Southern European Atlantic diet could promote healthy aging by means of epigenetic mechanisms. This review highlights the necessity of performing longitudinal studies to demonstrate this proposal.
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Affiliation(s)
- Paula M Lorenzo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Andrea G Izquierdo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Gemma Rodriguez-Carnero
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,Endocrinology and Nutrition Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Antía Fernández-Pombo
- Endocrinology and Nutrition Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Alba Iglesias
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Marcos C Carreira
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Molecular and Cellular Endocrinology Group. Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Cristina Tejera
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,Endocrinology and Nutrition Unit, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS), Ferrol, Spain
| | - Diego Bellido
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,Endocrinology and Nutrition Unit, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS), Ferrol, Spain
| | - Miguel A Martinez-Olmos
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Endocrinology and Nutrition Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rosaura Leis
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Department of Pediatrics, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS); Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain,Fundacion Dieta Atlántica, Santiago de Compostela, Spain
| | - Felipe F Casanueva
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Molecular and Cellular Endocrinology Group. Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain,Fundacion Dieta Atlántica, Santiago de Compostela, Spain
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29
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Taft DH, Lewis ZT, Nguyen N, Ho S, Masarweh C, Dunne-Castagna V, Tancredi DJ, Huda MN, Stephensen CB, Hinde K, von Mutius E, Kirjavainen PV, Dalphin JC, Lauener R, Riedler J, Smilowitz JT, German JB, Morrow AL, Mills DA. Bifidobacterium Species Colonization in Infancy: A Global Cross-Sectional Comparison by Population History of Breastfeeding. Nutrients 2022; 14:nu14071423. [PMID: 35406036 PMCID: PMC9003546 DOI: 10.3390/nu14071423] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/16/2022] Open
Abstract
Bifidobacterium species are beneficial and dominant members of the breastfed infant gut microbiome; however, their health benefits are partially species-dependent. Here, we characterize the species and subspecies of Bifidobacterium in breastfed infants around the world to consider the potential impact of a historic dietary shift on the disappearance of B. longum subsp. infantis in some populations. Across populations, three distinct patterns of Bifidobacterium colonization emerged: (1) The dominance of Bifidobacterium longum subspecies infantis, (2) prevalent Bifidobacterium of multiple species, and (3) the frequent absence of any Bifidobacterium. These patterns appear related to a country’s history of breastfeeding, with infants in countries with historically high rates of long-duration breastfeeding more likely to be colonized by B. longum subspecies infantis compared with infants in countries with histories of shorter-duration breastfeeding. In addition, the timing of infant colonization with B. longum subsp. infantis is consistent with horizontal transmission of this subspecies, rather than the vertical transmission previously reported for other Bifidobacterium species. These findings highlight the need to consider historical and cultural influences on the prevalence of gut commensals and the need to understand epidemiological transmission patterns of Bifidobacterium and other major commensals.
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Affiliation(s)
- Diana H. Taft
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
- Foods for Health Institute, University of California Davis, Davis, CA 95616, USA
| | - Zachery T. Lewis
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
| | - Nhu Nguyen
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
| | - Steve Ho
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
| | - Chad Masarweh
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
| | - Vanessa Dunne-Castagna
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
| | - Daniel J. Tancredi
- Department of Pediatrics, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - M. Nazmul Huda
- US Department of Agriculture, Western Human Nutrition Research Center, Davis, CA 95616, USA; (M.N.H.); (C.B.S.)
- Department of Nutrition, University of California Davis, Davis, CA 95616, USA
| | - Charles B. Stephensen
- US Department of Agriculture, Western Human Nutrition Research Center, Davis, CA 95616, USA; (M.N.H.); (C.B.S.)
- Department of Nutrition, University of California Davis, Davis, CA 95616, USA
| | - Katie Hinde
- Center for Evolution and Medicine, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA;
| | - Erika von Mutius
- Dr. von Hauner Children’s Hospital, Ludwig Maximilian University, 80337 Munich, Germany;
- Institute for Asthma and Allergy Prevention, Helmholtz Centre Munich, 85764 Neuherberg, Germany
| | - Pirkka V. Kirjavainen
- Environment Health Unit, National Institute for Health and Welfare, 70210 Kuopio, Finland;
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jean-Charles Dalphin
- Department of Respiratory Disease, UMR/CNRS 6249 Chrono-Environment, University Hospital of Besançon, F-25000 Besançon, France;
| | - Roger Lauener
- Christine Kühne-Center for Allergy Research and Education, 7265 Davos, Switzerland;
- Children’s Hospital of Eastern Switzerland, 9000 St. Gallen, Switzerland
| | - Josef Riedler
- Children’s Hospital Schwarzach, 5620 Schwarzach, Austria;
| | - Jennifer T. Smilowitz
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
- Foods for Health Institute, University of California Davis, Davis, CA 95616, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
- Foods for Health Institute, University of California Davis, Davis, CA 95616, USA
| | - Ardythe L. Morrow
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
- Correspondence: (A.L.M.); (D.A.M.); Tel.: +1-513-558-0809 (A.L.M.); +1-530-754-7821 (D.A.M.)
| | - David A. Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; (D.H.T.); (Z.T.L.); (N.N.); (S.H.); (C.M.); (V.D.-C.); (J.T.S.); (J.B.G.)
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Correspondence: (A.L.M.); (D.A.M.); Tel.: +1-513-558-0809 (A.L.M.); +1-530-754-7821 (D.A.M.)
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30
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Di Guglielmo MD, Franke KR, Robbins A, Crowgey EL. Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome. Front Cell Infect Microbiol 2022; 12:816601. [PMID: 35310842 PMCID: PMC8931315 DOI: 10.3389/fcimb.2022.816601] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/16/2022] [Indexed: 12/11/2022] Open
Abstract
Background Different feeding regimens in infancy alter the gastrointestinal (gut) microbial environment. The fecal microbiota in turn influences gastrointestinal homeostasis including metabolism, immune function, and extra-/intra-intestinal signaling. Advances in next generation sequencing (NGS) have enhanced our ability to study the gut microbiome of breast-fed (BF) and formula-fed (FF) infants with a data-driven hypothesis approach. Methods Next generation sequencing libraries were constructed from fecal samples of BF (n=24) and FF (n=10) infants and sequenced on an Illumina HiSeq 2500. Taxonomic classification of the NGS data was performed using the Sunbeam/Kraken pipeline and a functional analysis at the gene level was performed using publicly available algorithms, including BLAST, and custom scripts. Differentially represented genera, genes, and NCBI Clusters of Orthologous Genes (COG) were determined between cohorts using count data and R (statistical packages edgeR and DESeq2). Results Thirty-nine genera were found to be differentially represented between the BF and FF cohorts (FDR ≤ 0.01) including Parabacteroides, Enterococcus, Haemophilus, Gardnerella, and Staphylococcus. A Welch t-test of the Shannon diversity index for BF and FF samples approached significance (p=0.061). Bray-Curtis and Jaccard distance analyses demonstrated clustering and overlap in each analysis. Sixty COGs were significantly overrepresented and those most significantly represented in BF vs. FF samples showed dichotomy of categories representing gene functions. Over 1,700 genes were found to be differentially represented (abundance) between the BF and FF cohorts. Conclusions Fecal samples analyzed from BF and FF infants demonstrated differences in microbiota genera. The BF cohort includes greater presence of beneficial genus Bifidobacterium. Several genes were identified as present at different abundances between cohorts indicating differences in functional pathways such as cellular defense mechanisms and carbohydrate metabolism influenced by feeding. Confirmation of gene level NGS data via PCR and electrophoresis analysis revealed distinct differences in gene abundances associated with important biologic pathways.
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Affiliation(s)
- Matthew D. Di Guglielmo
- Division of General Academic Pediatrics, Department of Pediatrics, Nemours Children’s Health, Wilmington, DE, United States and Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
- *Correspondence: Matthew D. Di Guglielmo,
| | - Karl R. Franke
- Biomedical Research Department, Nemours Children’s Health, Wilmington, DE, United States
| | - Alan Robbins
- Biomedical Research Department, Nemours Children’s Health, Wilmington, DE, United States
| | - Erin L. Crowgey
- Biomedical Research Department, Nemours Children’s Health, Wilmington, DE, United States
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31
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Heiss BE, Ehrlich AM, Maldonado-Gomez MX, Taft DH, Larke JA, Goodson ML, Slupsky CM, Tancredi DJ, Raybould HE, Mills DA. Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. Gut Microbes 2022; 13:1986666. [PMID: 34705611 PMCID: PMC8555557 DOI: 10.1080/19490976.2021.1986666] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Understanding how exogenous microbes stably colonize the animal gut is essential to reveal mechanisms of action and tailor effective probiotic treatments. Bifidobacterium species are naturally enriched in the gastrointestinal tract of breast-fed infants. Human milk oligosaccharides (HMOs) are associated with this enrichment. However, direct mechanistic proof of the importance of HMOs in this colonization is lacking given milk contains additional factors that impact the gut microbiota. This study examined mice supplemented with the HMO 2'fucosyllactose (2'FL) together with a 2'FL-consuming strain, Bifidobacterium pseudocatenulatum MP80. 2'FL supplementation creates a niche for high levels of B.p. MP80 persistence, similar to Bifidobacterium levels seen in breast-fed infants. This synergism impacted gut microbiota composition, activated anti-inflammatory pathways and protected against chemically-induced colitis. These results demonstrate that bacterial-milk glycan interactions alone drive enrichment of beneficial Bifidobacterium and provide a model for tunable colonization thus facilitating insight into mechanisms of health promotion by bifidobacteriain neonates.
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Affiliation(s)
- Britta E. Heiss
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA
| | - Amy M. Ehrlich
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Maria X. Maldonado-Gomez
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA
| | - Diana H. Taft
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA
| | - Jules A. Larke
- Department of Nutrition, University of California-Davis, Davis, CA, USA
| | - Michael L. Goodson
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Carolyn M. Slupsky
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA,Department of Nutrition, University of California-Davis, Davis, CA, USA
| | - Daniel J. Tancredi
- Center for Healthcare Policy and Research, Department of Pediatrics, University of California-Davis, Sacramento, CA, USA
| | - Helen E. Raybould
- Foods for Health Institute, University of California-Davis, Davis, CA, USA,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA,CONTACT Helen E. Raybould Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - David A. Mills
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA,David A. Mills Department of Food Science and Technology, University of California-Davis, Davis, CA, USA
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32
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Why Are Bifidobacteria Important for Infants? Microorganisms 2022; 10:microorganisms10020278. [PMID: 35208736 PMCID: PMC8880231 DOI: 10.3390/microorganisms10020278] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
The presence of Bifidobacterium species in the maternal vaginal and fecal microbiota is arguably an evolutionary trait that allows these organisms to be primary colonizers of the newborn intestinal tract. Their ability to utilize human milk oligosaccharides fosters their establishment as core health-promoting organisms throughout life. A reduction in their abundance in infants has been shown to increase the prevalence of obesity, diabetes, metabolic disorder, and all-cause mortality later in life. Probiotic strains have been developed as supplements for premature babies and to counter some of these ailments as well as to confer a range of health benefits. The ability to modulate the immune response and produce short-chain fatty acids, particularly acetate and butyrate, that strengthen the gut barrier and regulate the gut microbiome, makes Bifidobacterium a core component of a healthy infant through adulthood.
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33
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Lebeaux RM, Karalis DB, Lee J, Whitehouse HC, Madan JC, Karagas MR, Hoen AG. The association between early life antibiotic exposure and the gut resistome of young children: a systematic review. Gut Microbes 2022; 14:2120743. [PMID: 36289062 PMCID: PMC9621065 DOI: 10.1080/19490976.2022.2120743] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/01/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance is a growing public health burden, but little is known about the effects of antibiotic exposure on the gut resistome. As childhood (0-5 years) represents a sensitive window of microbiome development and a time of relatively high antibiotic use, the aims of this systematic review were to evaluate the effects of antibiotic exposure on the gut resistome of young children and identify knowledge gaps. We searched PubMed, Scopus, Web of Science, and the Cochrane Central Register of Controlled Trials. A PICO framework was developed to determine eligibility criteria. Our main outcomes were the mean or median difference in overall resistance gene load and resistome alpha diversity by antibiotic exposure groups. Bias assessment was completed using RoB 2 and ROBINS-I with quality of evidence assessed via the GRADE criteria. From 4885 records identified, 14 studies (3 randomized controlled trials and 11 observational studies) were included in the qualitative review. Eight studies that included information on antibiotic exposure and overall resistance gene load reported no or positive associations. Inconsistent associations were identified for the nine studies that assessed resistome alpha diversity. We identified three main groups of studies based on study design, location, participants, antibiotic exposures, and indication for antibiotics. Overall, the quality of evidence for our main outcomes was rated low or very low, mainly due to potential bias from the selective of reporting results and confounding. We found evidence that antibiotic exposure is associated with changes to the overall gut resistance gene load of children and may influence the diversity of antimicrobial resistance genes. Given the overall quality of the studies, more research is needed to assess how antibiotics impact the resistome of other populations. Nonetheless, this evidence indicates that the gut resistome is worthwhile to consider for antibiotic prescribing practices.
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Affiliation(s)
- Rebecca M. Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Despina B. Karalis
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jihyun Lee
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Hanna C. Whitehouse
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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Sun Y, Xie R, Li L, Jin G, Zhou B, Huang H, Li M, Yang Y, Liu X, Cao X, Wang B, Liu W, Jiang K, Cao H. Prenatal Maternal Stress Exacerbates Experimental Colitis of Offspring in Adulthood. Front Immunol 2021; 12:700995. [PMID: 34804005 PMCID: PMC8595204 DOI: 10.3389/fimmu.2021.700995] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/13/2021] [Indexed: 01/14/2023] Open
Abstract
The prevalence of inflammatory bowel disease (IBD) is increasing worldwide and correlates with dysregulated immune response because of gut microbiota dysbiosis. Some adverse early life events influence the establishment of the gut microbiota and act as risk factors for IBD. Prenatal maternal stress (PNMS) induces gut dysbiosis and perturbs the neuroimmune network of offspring. In this study, we aimed to investigate whether PNMS increases the susceptibility of offspring to colitis in adulthood. The related index was assessed during the weaning period and adulthood. We found that PNMS impaired the intestinal epithelial cell proliferation, goblet cell and Paneth cell differentiation, and mucosal barrier function in 3-week-old offspring. PNMS induced low-grade intestinal inflammation, but no signs of microscopic inflammatory changes were observed. Although there was no pronounced difference between the PNMS and control offspring in terms of their overall measures of alpha diversity for the gut microbiota, distinct microbial community changes characterized by increases in Desulfovibrio, Streptococcus, and Enterococcus and decreases in Bifidobacterium and Blautia were induced in the 3-week-old PNMS offspring. Notably, the overgrowth of Desulfovibrio persisted from the weaning period to adulthood, consistent with the results observed using fluorescence in situ hybridization in the colon mucosa. Mechanistically, the fecal microbiota transplantation experiment showed that the gut microbiota from the PNMS group impaired the intestinal barrier function and induced low-grade inflammation. The fecal bacterial solution from the PNMS group was more potent than that from the control group in inducing inflammation and gut barrier disruption in CaCo-2 cells. After treatment with a TNF-α inhibitor (adalimumab), no statistical difference in the indicators of inflammation and intestinal barrier function was observed between the two groups. Finally, exposure to PNMS remarkably increased the values of the histopathological parameters and the inflammatory cytokine production in a mouse model of experimental colitis in adulthood. These findings suggest that PNMS can inhibit intestinal development, impair the barrier function, and cause gut dysbiosis characterized by the persistent overgrowth of Desulfovibrio in the offspring, resulting in exacerbated experimental colitis in adulthood.
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Affiliation(s)
- Yue Sun
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Runxiang Xie
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Lu Li
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Ge Jin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bingqian Zhou
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Huan Huang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Mengfan Li
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yunwei Yang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Wentian Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Kui Jiang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Abstract
The neonatal body provides a range of potential habitats, such as the gut, for microbes. These sites eventually harbor microbial communities (microbiotas). A "complete" (adult) gut microbiota is not acquired by the neonate immediately after birth. Rather, the exclusive, milk-based nutrition of the infant encourages the assemblage of a gut microbiota of low diversity, usually dominated by bifidobacterial species. The maternal fecal microbiota is an important source of bacterial species that colonize the gut of infants, at least in the short-term. However, development of the microbiota is influenced by the use of human milk (breast feeding), infant formula, preterm delivery of infants, caesarean delivery, antibiotic administration, family details and other environmental factors. Following the introduction of weaning (complementary) foods, the gut microbiota develops in complexity due to the availability of a diversity of plant glycans in fruits and vegetables. These glycans provide growth substrates for the bacterial families (such as members of the Ruminococcaceae and Lachnospiraceae) that, in due course, will dominate the gut microbiota of the adult. Although current data are often fragmentary and observational, it can be concluded that the nutrition that a child receives in early life is likely to impinge not only on the development of the microbiota at that time but also on the subsequent lifelong, functional relationships between the microbiota and the human host. The purpose of this review, therefore, is to discuss the importance of promoting the assemblage of functionally robust gut microbiotas at appropriate times in early life.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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36
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Pace RM, Williams JE, Robertson B, Lackey KA, Meehan CL, Price WJ, Foster JA, Sellen DW, Kamau-Mbuthia EW, Kamundia EW, Mbugua S, Moore SE, Prentice AM, Kita DG, Kvist LJ, Otoo GE, Ruiz L, Rodríguez JM, Pareja RG, McGuire MA, Bode L, McGuire MK. Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities. Microorganisms 2021; 9:1153. [PMID: 34072117 PMCID: PMC8230061 DOI: 10.3390/microorganisms9061153] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Previously published data from our group and others demonstrate that human milk oligosaccharide (HMOs), as well as milk and infant fecal microbial profiles, vary by geography. However, little is known about the geographical variation of other milk-borne factors, such as lactose and protein, as well as the associations among these factors and microbial community structures in milk and infant feces. Here, we characterized and contrasted concentrations of milk-borne lactose, protein, and HMOs, and examined their associations with milk and infant fecal microbiomes in samples collected in 11 geographically diverse sites. Although geographical site was strongly associated with milk and infant fecal microbiomes, both sample types assorted into a smaller number of community state types based on shared microbial profiles. Similar to HMOs, concentrations of lactose and protein also varied by geography. Concentrations of HMOs, lactose, and protein were associated with differences in the microbial community structures of milk and infant feces and in the abundance of specific taxa. Taken together, these data suggest that the composition of human milk, even when produced by relatively healthy women, differs based on geographical boundaries and that concentrations of HMOs, lactose, and protein in milk are related to variation in milk and infant fecal microbial communities.
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Affiliation(s)
- Ryan M. Pace
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - Janet E. Williams
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA; (J.E.W.); (M.A.M.)
| | - Bianca Robertson
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, Univeristy of California San Diego, La Jolla, CA 92093, USA; (B.R.); (L.B.)
- Department of Pediatrics, Univeristy of California San Diego, La Jolla, CA 92093, USA
| | - Kimberly A. Lackey
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - Courtney L. Meehan
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA;
| | - William J. Price
- Statistical Programs, College of Agricultural and Life Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - Daniel W. Sellen
- Department of Anthropology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | | | - Egidioh W. Kamundia
- Department of Human Nutrition, Egerton University, Nakuru 20115, Kenya; (E.W.K.-M.); (E.W.K.); (S.M.)
| | - Samwel Mbugua
- Department of Human Nutrition, Egerton University, Nakuru 20115, Kenya; (E.W.K.-M.); (E.W.K.); (S.M.)
| | - Sophie E. Moore
- Department of Women and Children’s Health, King’s College London, London WC2R 2LS, UK;
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, Gambia;
| | - Andrew M. Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, Gambia;
| | - Debela G. Kita
- Department of Anthropology, Hawassa University, Hawassa P.O. Box 27601, Ethiopia;
| | - Linda J. Kvist
- Faculty of Medicine, Lund University, 221 00 Lund, Sweden;
| | - Gloria E. Otoo
- Department of Nutrition and Food Science, University of Ghana, Accra 00233, Ghana;
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Juan M. Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain;
| | | | - Mark A. McGuire
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA; (J.E.W.); (M.A.M.)
| | - Lars Bode
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, Univeristy of California San Diego, La Jolla, CA 92093, USA; (B.R.); (L.B.)
- Department of Pediatrics, Univeristy of California San Diego, La Jolla, CA 92093, USA
| | - Michelle K. McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID 83844, USA;
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Kuwelker K, Langeland N, Löhr IH, Gidion J, Manyahi J, Moyo SJ, Blomberg B, Klingenberg C. Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial. Trials 2021; 22:312. [PMID: 33926519 PMCID: PMC8082054 DOI: 10.1186/s13063-021-05251-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/07/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) has emerged as an urgent global health threat and is by the World Health Organization ranked as priority 1 among pathogens in need of new treatment. Studies have shown high mortality in Tanzanian children with ESBL-E infections. Gut colonization of ESBL-E, which is a potential risk factor of ESBL-E infections, is reported to be very high among children in Tanzania. Probiotics may potentially reduce gut colonization of multidrug-resistant bacteria. However, there is limited data on whether probiotics may reduce ESBL-E carriage in infants. The ProRIDE Trial aims to evaluate whether the use of probiotics can reduce morbidity and mortality among infants in Haydom, Tanzania, and whether this effect is associated with a reduction in ESBL-E colonization and/or infections. METHODS/DESIGN This large randomized double-blinded placebo-controlled trial aims to recruit 2000 newborn infants at Haydom Lutheran Hospital and the surrounding area in the period of November 2020 to November 2021. Participants will be enrolled from days 0 to 3 after birth and randomized to receive probiotics or placebo for 4 weeks. Participants will be followed-up for 6 months, during which three visits will be made to collect clinical and demographic information, as well as rectal swabs and fecal samples which will be subjected to laboratory analysis. The primary composite outcome is the prevalence of death and/or hospitalization at 6 months of age. DISCUSSION As the use of probiotics may give a more favorable gut composition, and thereby improve health and reduce morbidity and mortality, the results may have implications for future therapy guidelines in Africa and internationally. TRIAL REGISTRATION ClinicalTrials.gov NCT04172012. Registered on November 21, 2019.
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Affiliation(s)
- Kanika Kuwelker
- Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Haukelandsbakken, 5009 Bergen, Norway
| | - Nina Langeland
- Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Haukelandsbakken, 5009 Bergen, Norway
- Department of Clinical Science, University of Bergen, Laboratory Building, Haukeland University Hospital, Jonas Lies veg 87, 5021 Bergen, Norway
| | - Iren Høyland Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Gerd Ragna Bloch Thorsens gate, 4011 Stavanger, Norway
| | - Joshua Gidion
- Department of Paediatrics, Haydom Lutheran Hospital, Mbulu, Manyara Tanzania
| | - Joel Manyahi
- Department of Clinical Science, University of Bergen, Laboratory Building, Haukeland University Hospital, Jonas Lies veg 87, 5021 Bergen, Norway
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, P.O. Box 65005, Dar es Salaam, Tanzania
| | - Sabrina John Moyo
- Department of Clinical Science, University of Bergen, Laboratory Building, Haukeland University Hospital, Jonas Lies veg 87, 5021 Bergen, Norway
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, P.O. Box 65005, Dar es Salaam, Tanzania
| | - Bjørn Blomberg
- Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Haukelandsbakken, 5009 Bergen, Norway
- Department of Clinical Science, University of Bergen, Laboratory Building, Haukeland University Hospital, Jonas Lies veg 87, 5021 Bergen, Norway
| | - Claus Klingenberg
- Department of Paediatrics and Adolescence Medicine, University Hospital of North Norway, Tromsø, Norway
- Paediatric Research Group, Faculty of Health Sciences, University of Tromsø-Arctic University of Norway, Tromsø, Norway
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38
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Muurinen J, Richert J, Wickware CL, Richert B, Johnson TA. Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential. Sci Rep 2021; 11:5485. [PMID: 33750827 PMCID: PMC7970892 DOI: 10.1038/s41598-021-84759-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Even though the use of antibiotics for food-producing animals may contribute to the emergence of antimicrobial resistance, antibiotics are still used as growth promoters. Due to consumer and regulatory pressures, the use of alternatives to antibiotics as growth promoters is increasing, thus more information is needed on their capability to disseminate antimicrobial resistance compared to antibiotics. We investigated the impacts of carbadox (antibiotic), copper sulfate and zinc oxide (metals) and mushroom powder (natural product) on the pig fecal resistome and microbiome. Antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using a high-throughput qPCR array with 382 primer pairs. Bacterial community composition was determined by 16S rRNA gene sequencing. More ARGs co-occurred with MGEs in the growth promoter group samples than in the control group samples. Community composition could not be linked to resistome in the growth promoter group samples, indicating a potential decoupling of ARGs and phylogeny. Additionally, machine-learning methods aided in defining the community and resistome differences in response to treatments. Since increased ARG mobility potential was the primary response to the dietary additives used in this study, we suggest that ARG mobility should be considered when designing antimicrobial use policies and antimicrobial resistance surveillances.
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Affiliation(s)
- Johanna Muurinen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
| | - Jacob Richert
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Carmen L Wickware
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Brian Richert
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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39
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Bassaganya-Riera J, Berry EM, Blaak EE, Burlingame B, le Coutre J, van Eden W, El-Sohemy A, German JB, Knorr D, Lacroix C, Muscaritoli M, Nieman DC, Rychlik M, Scholey A, Serafini M. Goals in Nutrition Science 2020-2025. Front Nutr 2021; 7:606378. [PMID: 33665201 PMCID: PMC7923694 DOI: 10.3389/fnut.2020.606378] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Five years ago, with the editorial board of Frontiers in Nutrition, we took a leap of faith to outline the Goals for Nutrition Science - the way we see it (1). Now, in 2020, we can put ourselves to the test and take a look back. Without a doubt we got it right with several of the key directions. To name a few, Sustainable Development Goals (SDGs) for Food and Nutrition are part of the global public agenda, and the SDGs contribute to the structuring of international science and research. Nutritional Science has become a critical element in strengthening work on the SDGs, and the development of appropriate methodologies is built on the groundwork of acquiring and analyzing big datasets. Investigation of the Human Microbiome is providing novel insight on the interrelationship between nutrition, the immune system and disease. Finally, with an advanced definition of the gut-brain-axis we are getting a glimpse into the potential for Nutrition and Brain Health. Various milestones have been achieved, and any look into the future will have to consider the lessons learned from Covid-19 and the sobering awareness about the frailty of our food systems in ensuring global food security. With a view into the coming 5 years from 2020 to 2025, the editorial board has taken a slightly different approach as compared to the previous Goals article. A mind map has been created to outline the key topics in nutrition science. Not surprisingly, when looking ahead, the majority of scientific investigation required will be in the areas of health and sustainability. Johannes le Coutre, Field Chief Editor, Frontiers in Nutrition.
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Affiliation(s)
- Josep Bassaganya-Riera
- Nutritional Immunology and Molecular Medicine Laboratory (NIMML) Institute, Blacksburg, VA, United States
| | - Elliot M Berry
- Braun School of Public Health, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Ellen E Blaak
- Department of Human Biology, Maastricht University, Maastricht, Netherlands
| | | | - Johannes le Coutre
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Willem van Eden
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, Davis, CA, United States
| | - Dietrich Knorr
- Institute of Food Technology and Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Christophe Lacroix
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Maurizio Muscaritoli
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - David C Nieman
- Human Performance Laboratory, Department of Biology, Appalachian State University, Kannapolis, NC, United States
| | - Michael Rychlik
- Technical University of Munich, Analytical Food Chemistry, Freising, Germany
| | - Andrew Scholey
- Centre for Human Psychopharmacology, Swinburne University, Melbourne, VIC, Australia
| | - Mauro Serafini
- Functional Food and Metabolic Stress Prevention Laboratory, Faculty of Biosciences and Technologies for Agriculture, Food and Environment, University of Teramo, Teramo, Italy
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40
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Ruby E. Getting to know our microbial friends by dropping into their neighbourhood. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:27-30. [PMID: 33047473 DOI: 10.1111/1758-2229.12895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Edward Ruby
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
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41
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Casaburi G, Duar RM, Brown H, Mitchell RD, Kazi S, Chew S, Cagney O, Flannery RL, Sylvester KG, Frese SA, Henrick BM, Freeman SL. Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States. Sci Rep 2021; 11:1472. [PMID: 33479326 PMCID: PMC7820601 DOI: 10.1038/s41598-020-80583-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
The gut microbiome plays an important role in early life, protecting newborns from enteric pathogens, promoting immune system development and providing key functions to the infant host. Currently, there are limited data to broadly assess the status of the US healthy infant gut microbiome. To address this gap, we performed a multi-state metagenomic survey and found high levels of bacteria associated with enteric inflammation (e.g. Escherichia, Klebsiella), antibiotic resistance genes, and signatures of dysbiosis, independent of location, age, and diet. Bifidobacterium were less abundant than generally expected and the species identified, including B. breve, B. longum and B. bifidum, had limited genetic capacity to metabolize human milk oligosaccharides (HMOs), while B. infantis strains with a complete capacity for HMOs utilization were found to be exceptionally rare. Considering microbiome composition and functional capacity, this survey revealed a previously unappreciated dysbiosis that is widespread in the contemporary US infant gut microbiome.
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Affiliation(s)
| | | | | | | | - Sufyan Kazi
- Evolve BioSystems, Inc., Davis, CA, 95618, USA
| | | | - Orla Cagney
- Evolve BioSystems, Inc., Davis, CA, 95618, USA
| | | | | | - Steven A Frese
- Evolve BioSystems, Inc., Davis, CA, 95618, USA.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE, 68588, USA.,Department of Nutrition, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Bethany M Henrick
- Evolve BioSystems, Inc., Davis, CA, 95618, USA.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE, 68588, USA
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42
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Nadimpalli ML, Bourke CD, Robertson RC, Delarocque-Astagneau E, Manges AR, Pickering AJ. Can breastfeeding protect against antimicrobial resistance? BMC Med 2020; 18:392. [PMID: 33317529 PMCID: PMC7737306 DOI: 10.1186/s12916-020-01862-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The proportion of infections among young children that are antimicrobial-resistant is increasing across the globe. Newborns may be colonized with enteric antimicrobial-resistant pathogens early in life, which is a risk factor for infection-related morbidity and mortality. Breastfeeding is actively promoted worldwide for its beneficial impacts on newborn health and gut health. However, the role of breastfeeding and human milk components in mitigating young children's carriage of antimicrobial-resistant pathogens and antibiotic resistance genes has not been comprehensively explored. MAIN BODY Here, we review how the act of breastfeeding, early breastfeeding, and/or human milk components, such as the milk microbiota, secretory IgA, human milk oligosaccharides, antimicrobial peptides, and microRNA -bearing extracellular vesicles, could play a role in preventing the establishment of antimicrobial-resistant pathogens in young children's developing gut microbiomes. We describe findings from recent human studies that support this concept. CONCLUSION Given the projected rise in global morbidity and mortality that will stem from antimicrobial-resistant infections, identifying behavioral or nutritional interventions that could decrease children's susceptibility to colonization with antimicrobial-resistant pathogens may be one strategy for protecting their health. We suggest that breastfeeding and human milk supplements deserve greater attention as potential preventive measures in the global effort to combat antimicrobial resistance, particularly in low- and middle-income settings.
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Affiliation(s)
- Maya L Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Science & Engineering Complex, Anderson Hall, Room 204, 200 College Avenue, Medford, MA, USA. .,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA.
| | - Claire D Bourke
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.,Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Ruairi C Robertson
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Elisabeth Delarocque-Astagneau
- Université Paris-Saclay, UVSQ, Inserm, CESP, Team Anti-infective Evasion and Pharmacoepidemiology, 78180 Montigny, France.,AP-HP, GHU Paris Saclay University, Raymond Poincaré Hospital, Epidemiology and Public Health Department, 92380 Garches, France
| | - Amee R Manges
- School of Population and Public Health, The University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Amy J Pickering
- Department of Civil and Environmental Engineering, Tufts University, Science & Engineering Complex, Anderson Hall, Room 204, 200 College Avenue, Medford, MA, USA.,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
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43
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Wallace MJ, Fishbein SRS, Dantas G. Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. Gut Microbes 2020; 12:1799654. [PMID: 32772817 PMCID: PMC7524338 DOI: 10.1080/19490976.2020.1799654] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antimicrobial resistance is one of the largest threats to global health and imposes substantial burdens in terms of morbidity, mortality, and economic costs. The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. Furthermore, various environmental reservoirs and stressors facilitate the evolution and transmission of resistance. In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. Importantly, we present emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms.
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Affiliation(s)
- M. J. Wallace
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - S. R. S. Fishbein
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - G. Dantas
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA,CONTACT G. Dantas Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
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Alcon-Giner C, Dalby MJ, Caim S, Ketskemety J, Shaw A, Sim K, Lawson MA, Kiu R, Leclaire C, Chalklen L, Kujawska M, Mitra S, Fardus-Reid F, Belteki G, McColl K, Swann JR, Kroll JS, Clarke P, Hall LJ. Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study. CELL REPORTS MEDICINE 2020; 1:100077. [PMID: 32904427 PMCID: PMC7453906 DOI: 10.1016/j.xcrm.2020.100077] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/28/2020] [Accepted: 07/31/2020] [Indexed: 12/11/2022]
Abstract
Supplementation with members of the early-life microbiota as “probiotics” is increasingly used in attempts to beneficially manipulate the preterm infant gut microbiota. We performed a large observational longitudinal study comprising two preterm groups: 101 infants orally supplemented with Bifidobacterium and Lactobacillus (Bif/Lacto) and 133 infants non-supplemented (control) matched by age, sex, and delivery method. 16S rRNA gene profiling on fecal samples (n = 592) showed a predominance of Bifidobacterium and a lower abundance of pathobionts in the Bif/Lacto group. Metabolomic analysis showed higher fecal acetate and lactate and a lower fecal pH in the Bif/Lacto group compared to the control group. Fecal acetate positively correlated with relative abundance of Bifidobacterium, consistent with the ability of the supplemented Bifidobacterium strain to metabolize human milk oligosaccharides into acetate. This study demonstrates that microbiota supplementation is associated with a Bifidobacterium-dominated preterm microbiota and gastrointestinal environment more closely resembling that of full-term infants. Bifidobacterium dominates the gut microbiota in supplemented preterm infants Supplemented preterm infants have lower abundance of potential pathobionts Metabolomic analysis show higher fecal acetate and lower pH in supplemented infants In vitro and genomic analysis confirm HMO metabolism in Bifidobacterium supplement
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Affiliation(s)
- Cristina Alcon-Giner
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Matthew J. Dalby
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Shabhonam Caim
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jennifer Ketskemety
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Alex Shaw
- Department of Medicine, Section of Pediatrics, Imperial College London, London, UK
| | - Kathleen Sim
- Department of Medicine, Section of Pediatrics, Imperial College London, London, UK
| | - Melissa A.E. Lawson
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Raymond Kiu
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Charlotte Leclaire
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lisa Chalklen
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Suparna Mitra
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Fahmina Fardus-Reid
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Gustav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katherine McColl
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospital, Norwich, UK
| | - Jonathan R. Swann
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - J. Simon Kroll
- Department of Medicine, Section of Pediatrics, Imperial College London, London, UK
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J. Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, Freising, Germany
- ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
- Corresponding author
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45
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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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Brink LR, Mercer KE, Piccolo BD, Chintapalli SV, Elolimy A, Bowlin AK, Matazel KS, Pack L, Adams SH, Shankar K, Badger TM, Andres A, Yeruva L. Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Am J Clin Nutr 2020; 111:1190-1202. [PMID: 32330237 PMCID: PMC7266684 DOI: 10.1093/ajcn/nqaa076] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/26/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neonatal diet has a large influence on child health and might modulate changes in fecal microbiota and metabolites. OBJECTIVES The aim is to investigate fecal microbiota and metabolites at different ages in infants who were breastfed (BF), received dairy-based milk formula (MF), or received soy-based formula (SF). METHODS Fecal samples were collected at 3 (n = 16, 12, and 14, respectively), 6 (n = 20, 19, and 15, respectively), 9 (n = 12, 11, and 12, respectively), and 12 mo (n = 14, 14, and 15, respectively) for BF, MF, and SF infants. Infants that breastfed until 9 mo and switched to formula were considered as no longer breastfeeding at 12 mo. Microbiota data were obtained using 16S ribosomal RNA sequencing. Untargeted metabolomics was conducted using a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer. The data were analyzed using R (version 3.6.0) within the RStudio (version 1.1.463) platform. RESULTS At 3, 6, and 9 mo of age BF infants had the lowest α-diversity, SF infants had the highest diversity, and MF was intermediate. Bifidobacterium was 2.6- to 5-fold lower in SF relative to BF infants through 1 y of life. An unidentified genus from Ruminococcaceae higher in the SF (2%) than in the MF (0.4%) and BF (0.08%) infants at 3 mo of age was observed. In BF infants higher levels of butyric acid, d-sphingosine, kynurenic acid, indole-3-lactic acid, indole-3-acetic acid, and betaine were observed than in MF and SF infants. At 3 mo Ruminococcaceae was positively correlated to azelaic, gentisic, isocitric, sebacic, and syringic acids. At 6 mo Oscillospira was negatively correlated with 3-hydroxybutyric-acid, hydroxy-hydrocinnamic acid, and betaine whereas Bifidobacterium was negatively associated with 5-hydroxytryptamine. At 12 mo of age, Lachnospiraceae was negatively associated with hydroxyphenyllactic acid. CONCLUSIONS Infant diet has a large impact on the fecal microbiome and metabolome in the first year of life.This study was registered at clinicaltrials.gov as NCT00616395.
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Affiliation(s)
- Lauren R Brink
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kelly E Mercer
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian D Piccolo
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ahmed Elolimy
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Anne K Bowlin
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Katelin S Matazel
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Lindsay Pack
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sean H Adams
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kartik Shankar
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Thomas M Badger
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Aline Andres
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Laxmi Yeruva
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
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Galacto- and Fructo-oligosaccharides Utilized for Growth by Cocultures of Bifidobacterial Species Characteristic of the Infant Gut. Appl Environ Microbiol 2020; 86:AEM.00214-20. [PMID: 32220841 DOI: 10.1128/aem.00214-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023] Open
Abstract
Bifidobacterial species are common inhabitants of the gut of human infants during the period when milk is a major component of the diet. Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium longum subspecies longum, and B. longum subspecies infantis have been detected frequently in infant feces, but B. longum subsp. infantis may be disadvantaged numerically in the gut of infants in westernized countries. This may be due to the different durations of breast milk feeding in different countries. Supplementation of the infant diet or replacement of breast milk using formula feeds is common in Western countries. Formula milks often contain galacto- and/or fructo-oligosaccharides (GOS and FOS, respectively) as additives to augment the concentration of oligosaccharides in ruminant milks, but the ability of B. longum subsp. infantis to utilize these potential growth substrates when they are in competition with other bifidobacterial species is unknown. We compared the growth and oligosaccharide utilization of GOS and FOS by bifidobacterial species in pure culture and coculture. Short-chain GOS and FOS (degrees of polymerization [DP] 2 and 3) were favored growth substrates for strains of B. bifidum and B. longum subsp. longum, whereas both B. breve and B. longum subsp. infantis had the ability to utilize both short- and longer-chain GOS and FOS (DP 2 to 6). B. breve was nevertheless numerically dominant over B. longum subsp. infantis in cocultures. This was probably related to the slower use of GOS of DP 3 by B. longum subsp. infantis, indicating that the kinetics of substrate utilization is an important ecological factor in the assemblage of gut communities.IMPORTANCE The kinds of bacteria that form the collection of microbes (the microbiota) in the gut of human infants may influence health and well-being. Knowledge of how the composition of the infant diet influences the assemblage of the bacterial collection is therefore important because dietary interventions may offer opportunities to alter the microbiota with the aim of improving health. Bifidobacterium longum subspecies infantis is a well-known bacterial species, but under modern child-rearing conditions it may be disadvantaged in the gut. Modern formula milks often contain particular oligosaccharide additives that are generally considered to support bifidobacterial growth. However, studies of the ability of various bifidobacterial species to grow together in the presence of these oligosaccharides have not been conducted. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of human nutrition on the development of the gut microbiota.
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Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies. Microorganisms 2020; 8:microorganisms8050760. [PMID: 32438679 PMCID: PMC7285294 DOI: 10.3390/microorganisms8050760] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Correct establishment of the gut microbiome is compromised in premature babies, with Bifidobacterium being one of the most affected genera. Prematurity often entails the inability to successfully breastfeed, therefore requiring the implementation of other feeding modes; breast milk expression from a donor mother is the recommended option when their own mother’s milk is not available. Some studies showed different gut microbial profiles in premature infants fed with breast milk and donor human milk, however, it is not known how this affects the species composition of the genus Bifidobacterium. The objective of this study was to assess the effect of donated human milk on shaping the gut bifidobacterial populations of premature babies during the first three months of life. We analyzed the gut bifidobacterial communities of 42 premature babies fed with human donor milk or own-mother milk by the 16S rRNA–23S rRNA internal transcriber spaces (ITS) region sequencing and q-PCR. Moreover, metabolic activity was assessed by gas chromatography. We observed a specific bifidobacterial profile based on feeding type, with higher bifidobacterial diversity in the human donor milk group. Differences in specific Bifidobacterium species composition may contribute to the development of specific new strategies or treatments aimed at mimicking the impact of own-mother milk feeding in neonatal units.
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49
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Swann JR, Spitzer SO, Diaz Heijtz R. Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Metabolites 2020; 10:metabo10050172. [PMID: 32344839 PMCID: PMC7281085 DOI: 10.3390/metabo10050172] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 01/23/2023] Open
Abstract
The gut microbiome is recognized to exert a wide-ranging influence on host health and disease, including brain development and behavior. Commensal bacteria can produce bioactive molecules that enter the circulation and impact host physiology and homeostasis. However, little is known about the potential for these metabolites to cross the blood–brain barrier and enter the developing brain under normal physiological conditions. In this study, we used a liquid chromatography–mass spectrometry-based metabolomic approach to characterize the developmental profiles of microbial-derived metabolites in the forebrains of mice across three key postnatal developmental stages, co-occurring with the maturation of the gut microbiota. We demonstrate that direct metabolites of the gut microbiome (e.g., imidazole propionate) or products of the combinatorial metabolism between the microbiome and host (e.g., 3-indoxyl-sulfate, trimethylamine-N-oxide, and phenylacetylglycine) are present in the forebrains of mice as early as the neonatal period and remain into adulthood. These findings demonstrate that microbial-associated molecules can cross the BBB either in their detected form or as precursor molecules that undergo further processing in the brain. These chemical messengers are able to bind receptors known to be expressed in the brain. Alterations in the gut microbiome may therefore influence neurodevelopmental trajectories via the regulation of these microbial-associated metabolites.
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Affiliation(s)
- Jonathan R. Swann
- School of Human Development and Health, Faculty of Medicine, University of Southampton, University Road, Southampton SO17 1BJ, UK
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
- Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden
- Correspondence: (J.R.S.); (R.D.H.)
| | - Sonia O. Spitzer
- The Francis Crick Institute, London, 1 Midland Rd, London NW1 1AT, UK
| | - Rochellys Diaz Heijtz
- Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden
- INSERM U1239, University of Rouen, Normandy, 76130 Mont-Saint-Aignan, France
- Correspondence: (J.R.S.); (R.D.H.)
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50
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Duar RM, Henrick BM, Casaburi G, Frese SA. Integrating the Ecosystem Services Framework to Define Dysbiosis of the Breastfed Infant Gut: The Role of B. infantis and Human Milk Oligosaccharides. Front Nutr 2020; 7:33. [PMID: 32346537 PMCID: PMC7171047 DOI: 10.3389/fnut.2020.00033] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/05/2020] [Indexed: 12/17/2022] Open
Abstract
Mounting evidence supports a connection between the composition of the infant gut microbiome and long-term health. In fact, aberrant microbiome compositions during key developmental windows in early life are associated with increased disease risk; therefore, making pertinent modifications to the microbiome during infancy offers significant promise to improve human health. There is growing support for integrating the concept of ecosystem services (the provision of benefits from ecosystems to humans) in linking specific microbiome functions to human well-being. This framework is widely applied in conservation efforts of macro-ecosystems and offers a systematic approach to guide restoration actions aimed to recover critical ecological functions. The aim of this work is to apply the ecosystem services framework to integrate recent studies demonstrating stable alteration of the gut microbiome of breastfed infants when Bifidobacterium longum subsp. infantis EVC001, a gut symbiont capable of efficiently utilizing human milk oligosaccharides into organic acids that are beneficial for the infant and lower intestinal pH, is reintroduced. Additionally, using examples from the literature we illustrate how the absence of B. infantis results in diminished ecosystem services, which may be associated with health consequences related to immune and metabolic disorders. Finally, we propose a model by which infant gut dysbiosis can be defined as a reduction in ecosystem services supplied to the host by the gut microbiome rather than merely changes in diversity or taxonomic composition. Given the increased interest in targeted microbiome modification therapies to decrease acute and chronic disease risk, the model presented here provides a framework to assess the effectiveness of such strategies from a host-centered perspective.
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Affiliation(s)
| | - Bethany M Henrick
- Evolve BioSystems, Inc., Davis, CA, United States.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE, United States
| | | | - Steven A Frese
- Evolve BioSystems, Inc., Davis, CA, United States.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE, United States
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