1
|
Mukherjee A, Breselge S, Dimidi E, Marco ML, Cotter PD. Fermented foods and gastrointestinal health: underlying mechanisms. Nat Rev Gastroenterol Hepatol 2024; 21:248-266. [PMID: 38081933 DOI: 10.1038/s41575-023-00869-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 12/20/2023]
Abstract
Although fermentation probably originally developed as a means of preserving food substrates, many fermented foods (FFs), and components therein, are thought to have a beneficial effect on various aspects of human health, and gastrointestinal health in particular. It is important that any such perceived benefits are underpinned by rigorous scientific research to understand the associated mechanisms of action. Here, we review in vitro, ex vivo and in vivo studies that have provided insights into the ways in which the specific food components, including FF microorganisms and a variety of bioactives, can contribute to health-promoting activities. More specifically, we draw on representative examples of FFs to discuss the mechanisms through which functional components are produced or enriched during fermentation (such as bioactive peptides and exopolysaccharides), potentially toxic or harmful compounds (such as phytic acid, mycotoxins and lactose) are removed from the food substrate, and how the introduction of fermentation-associated live or dead microorganisms, or components thereof, to the gut can convey health benefits. These studies, combined with a deeper understanding of the microbial composition of a wider variety of modern and traditional FFs, can facilitate the future optimization of FFs, and associated microorganisms, to retain and maximize beneficial effects in the gut.
Collapse
Affiliation(s)
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Eirini Dimidi
- Department of Nutritional Sciences, King's College London, London, UK
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, CA, USA
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
- VistaMilk, Cork, Ireland.
| |
Collapse
|
2
|
Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R. Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study. Microorganisms 2023; 11:2437. [PMID: 37894093 PMCID: PMC10608849 DOI: 10.3390/microorganisms11102437] [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: 08/20/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported. METHODS The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry. RESULTS Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM). CONCLUSIONS Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.
Collapse
Affiliation(s)
- Reham Magdy Wasfy
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Babacar Mbaye
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Patrick Borentain
- Unité Hépatologie, Hôpital de la Timone, APHM, 13005 Marseille, France;
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Maria Leticia Murillo Ruiz
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Aurelia Caputo
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Claudia Andrieu
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Nicholas Armstrong
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Rene Gerolami
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
- Unité Hépatologie, Hôpital de la Timone, APHM, 13005 Marseille, France;
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| |
Collapse
|
3
|
Botha NN, Ansah EW, Segbedzi CE, Darkwa S. Public health concerns for food contamination in Ghana: A scoping review. PLoS One 2023; 18:e0288685. [PMID: 37561804 PMCID: PMC10414628 DOI: 10.1371/journal.pone.0288685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
Nutrition is sturdily and rapidly becoming the foremost determinant of health in today's Sars-Cov-2 and climate change ravaged world. While safe food sustains life, contamination obliterates its values and could result in death and short to long term morbidity. The purpose of this scoping review is to explore food contamination in Ghana, between 2001-2022. Using Arksey and O'Malley's procedure, a systematic literature search from PubMed, JSTOR, ScienceDirect, ProQuest, Scopus, Emeralds Insight, Google Scholar, and Google was carried out. Following the inclusion criteria, 40 published and grey literature were covered in this review. The review revealed the following: Studies on food contamination involving Greater Accra, Ashanti, Central, and Eastern Regions alone account for over 50% of the total number of such studies conducted in Ghana; regulators failed in enforcing regulations, monitoring and supervision; managers failed to provide adequate infrastructure and facilities. The most common food safety risks of public health concern are: i) micro-organisms (E. coli/faecal coliforms, Staphylococcus aureus, Salmonella spp, Bacillus cereus, and Viral hepatitis); ii) drugs (Amoxicillin, Chlortetracycline, Ciprofloxacin, Danofloxacin, and Doxycycline) and; iii) chemicals (Chlorpyrifos). Salad, vegetables, sliced mango, meat pie, and snail khebab are of high public health risks. The following deductions were made from the review: Highly contaminated food results in death, short to long term morbidity, economic loss, and threatens to displace Ghana's efforts at achieving the Sustainable Development Goals (SDG) 2. Thus, Government must resource key regulatory bodies to enhance their operational capacity, regulators must foster collaboration in monitoring and supervision of food vendors, and managers of food service outlets must provide adequate facilities to engender food safety culture.
Collapse
Affiliation(s)
- Nkosi Nkosi Botha
- Department of Health, Physical Education and Recreation (HPER), University of Cape Coast, Cape Coast, Ghana
| | - Edward Wilson Ansah
- Department of Health, Physical Education and Recreation (HPER), University of Cape Coast, Cape Coast, Ghana
| | - Cynthia Esinam Segbedzi
- Department of Health, Physical Education and Recreation (HPER), University of Cape Coast, Cape Coast, Ghana
| | - Sarah Darkwa
- Department of Vocational and Technical Education (VOTEC), University of Cape Coast, Cape Coast, Ghana
| |
Collapse
|
4
|
Chioma Mgbodile F, Nwagu TNT. Probiotic therapy, African fermented foods and food-derived bioactive peptides in the management of SARS-CoV-2 cases and other viral infections. BIOTECHNOLOGY REPORTS 2023; 38:e00795. [PMID: 37041970 PMCID: PMC10066861 DOI: 10.1016/j.btre.2023.e00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/04/2023]
Abstract
The current paper focuses on the impact of probiotics, African fermented foods and bioactive peptides on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection severity and related viral infections. Using probiotics or bioactive peptides as therapeutic adjuncts appears superior to standard care alone. Probiotics play critical roles in innate and adaptive immune modulation by balancing the gut microbiota to combat viral infections, secondary bacterial infections and microbial dysbiosis. African fermented foods contain abundant potential probiotic microorganisms such as the lactic acid bacteria (LAB), Saccharomyces, and Bacillus. More so, fermented food-derived bioactive peptides play vital roles in preventing cardiovascular diseases, hypertension, lung injury, diabetes, and other COVID-19 comorbidities. Regularly incorporating potential probiotics and bioactive peptides into diets should enable a build-up of the benefits in the body system that may result in a better prognosis, especially in COVID-19 patients with underlying complexities. Despite the reported therapeutic potentials of probiotics and fermented foods, numerous setbacks exist regarding their application in disease management. These shortfalls underscore an evident need for more studies to evaluate the specific potentials of probiotics and traditional fermented foods in ameliorating SARS-CoV-2 and other viral infections.
Collapse
|
5
|
Al KF, Chmiel JA, Stuivenberg GA, Reid G, Burton JP. Long-Duration Space Travel Support Must Consider Wider Influences to Conserve Microbiota Composition and Function. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081163. [PMID: 36013342 PMCID: PMC9409767 DOI: 10.3390/life12081163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022]
Abstract
The microbiota is important for immune modulation, nutrient acquisition, vitamin production, and other aspects for long-term human health. Isolated model organisms can lose microbial diversity over time and humans are likely the same. Decreasing microbial diversity and the subsequent loss of function may accelerate disease progression on Earth, and to an even greater degree in space. For this reason, maintaining a healthy microbiome during spaceflight has recently garnered consideration. Diet, lifestyle, and consumption of beneficial microbes can shape the microbiota, but the replenishment we attain from environmental exposure to microbes is important too. Probiotics, prebiotics, fermented foods, fecal microbiota transplantation (FMT), and other methods of microbiota modulation currently available may be of benefit for shorter trips, but may not be viable options to overcome the unique challenges faced in long-term space travel. Novel fermented food products with particular impact on gut health, immune modulation, and other space-targeted health outcomes are worthy of exploration. Further consideration of potential microbial replenishment to humans, including from environmental sources to maintain a healthy microbiome, may also be required.
Collapse
Affiliation(s)
- Kait F. Al
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
| | - John A. Chmiel
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
| | - Gerrit A. Stuivenberg
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
| | - Gregor Reid
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
- Department of Surgery, University of Western Ontario, London, ON N6A 4V2, Canada
- Lawson Health Research Institute, London, ON N6A 4V2, Canada
| | - Jeremy P. Burton
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
- Department of Surgery, University of Western Ontario, London, ON N6A 4V2, Canada
- Lawson Health Research Institute, London, ON N6A 4V2, Canada
- Correspondence:
| |
Collapse
|
6
|
Marco ML, Hutkins R, Hill C, Fulgoni VL, Cifelli CJ, Gahche J, Slavin JL, Merenstein D, Tancredi DJ, Sanders ME. A Classification System for Defining and Estimating Dietary Intake of Live Microbes in US Adults and Children. J Nutr 2022; 152:1729-1736. [PMID: 35583208 PMCID: PMC9258558 DOI: 10.1093/jn/nxac074] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Consuming live microbes in foods may benefit human health. Live microbe estimates have not previously been associated with individual foods in dietary databases. OBJECTIVES We aimed to estimate intake of live microbes in US children (aged 2-18 y) and adults (≥19 y) (n = 74,466; 51.2% female). METHODS Using cross-sectional data from the NHANES (2001-2018), experts assigned foods an estimated level of live microbes per gram [low (Lo), <104 CFU/g; medium (Med), 104-107 CFU/g; or high (Hi), >107 CFU/g]. Probiotic dietary supplements were also assessed. The mean intake of each live microbe category and the percentages of subjects who ate from each live microbe category were determined. Nutrients from foods with live microbes were also determined using the population ratio method. Because the Hi category comprised primarily fermented dairy foods, we also looked at aggregated data for Med or Hi (MedHi), which included an expanded range of live microbe-containing foods, including fruits and vegetables. RESULTS Our analysis showed that 52%, 20%, and 59% of children/adolescents, and 61%, 26%, and 67% of adults, consumed Med, Hi, or MedHi foods, respectively. Per capita intake of Med, Hi, and MedHi foods was 69, 16, and 85 g/d for children/adolescents, and 106, 21, and 127 g/d for adults, respectively. The proportion of subjects who consumed live microbes and overall per capita intake increased significantly over the 9 cycles/18-y study period (0.9-3.1 g/d per cycle in children across categories and 1.4 g/d per cycle in adults for the Med category). CONCLUSIONS This study indicated that children, adolescents, and adults in the United States steadily increased their consumption of foods with live microbes between the earliest (2001-2002) and latest (2017-2018) survey cycles. Additional research is needed to determine the relations between exposure to live microbes in foods and specific health outcomes or biomarkers.
Collapse
Affiliation(s)
- Maria L Marco
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | | | - Jaime Gahche
- Office of Dietary Supplements, NIH, Bethesda, MD, USA
| | - Joanne L Slavin
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Daniel Merenstein
- Department of Family Medicine, Georgetown University School of Medicine, Washington, DC, USA
| | - Daniel J Tancredi
- Department of Pediatrics, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Mary E Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| |
Collapse
|
7
|
Isenring J, Stevens MJA, Jans C, Lacroix C, Geirnaert A. Identification of Valerate as Carrying Capacity Modulator by Analyzing Lactiplantibacillus plantarum Colonization of Colonic Microbiota in vitro. Front Microbiol 2022; 13:910609. [PMID: 35722334 PMCID: PMC9197689 DOI: 10.3389/fmicb.2022.910609] [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: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Humans ingest many microorganisms, which may colonize and interact with the resident gut microbiota. However, extensive knowledge about host-independent microbe-microbe interactions is lacking. Here, we investigated such colonization process using a derivative of the model probiotic Lactiplantibacillus plantarum WCFS1 into continuously cultivated gut microbiota in the intestinal PolyFermS fermentation model inoculated with five independently immobilized human adult fecal microbiota. L. plantarum successfully colonized and organized itself spatially in the planktonic, that is, the reactor effluent, and sessile, that is, reactor biofilm, fractions of distinct human adult microbiota. The microbiota carrying capacity for L. plantarum was independent of L. plantarum introduction dose and second supplementation. Adult microbiota (n = 3) dominated by Prevotella and Ruminoccocus exhibited a higher carrying capacity than microbiota (n = 2) dominated by Bacteroides with 105 and 103 CFU/ml of L. plantarum, respectively. Cultivation of human adult microbiota over 3 months resulted in decreased carrying capacity and correlated positively with richness and evenness, suggesting enhanced resistance toward colonizers. Our analyses ultimately allowed us to identify the fermentation metabolite valerate as a modulator to increase the carrying capacity in a microbiota-independent manner. In conclusion, by uncoupling microbe-microbe interactions from host factors, we showed that L. plantarum colonizes the in vitro colonic community in a microbiota-dependent manner. We were further able to demonstrate that L. plantarum colonization levels were not susceptible to the introduction parameters dose and repeated administration but to microbiota features. Such knowledge is relevant in gaining a deeper ecological understanding of colonizer-microbiota interactions and developing robust probiotic strategies.
Collapse
Affiliation(s)
- Julia Isenring
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,Institute for Food Hygiene and Safety, University of Zürich, Zürich, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
8
|
Leeuwendaal NK, Stanton C, O’Toole PW, Beresford TP. Fermented Foods, Health and the Gut Microbiome. Nutrients 2022; 14:nu14071527. [PMID: 35406140 PMCID: PMC9003261 DOI: 10.3390/nu14071527] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/12/2022] Open
Abstract
Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.
Collapse
Affiliation(s)
| | - Catherine Stanton
- Teagasc Food Research Centre, P61 C996 Cork, Ireland; (N.K.L.); (C.S.)
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Paul W. O’Toole
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Tom P. Beresford
- Teagasc Food Research Centre, P61 C996 Cork, Ireland; (N.K.L.); (C.S.)
- Correspondence:
| |
Collapse
|
9
|
Dębińska A, Sozańska B. Fermented Food in Asthma and Respiratory Allergies—Chance or Failure? Nutrients 2022; 14:nu14071420. [PMID: 35406034 PMCID: PMC9002914 DOI: 10.3390/nu14071420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 01/27/2023] Open
Abstract
In the last few decades, a dramatic increase in the global prevalence of allergic diseases and asthma was observed. It was hypothesized that diet may be an important immunomodulatory factor influencing susceptibility to allergic diseases. Fermented food, a natural source of living microorganisms and bioactive compounds, has been demonstrated to possess health-promoting potentials and seems to be a promising strategy to reduce the risk of various immune-related diseases, such as allergic diseases and asthma. The exact mechanisms by which allergic diseases and asthma can be alleviated or prevented by fermented food are not well understood; however, its potential to exert an effect through modulating the immune response and influencing the gut microbiota has been recently studied. In this review, we provide the current knowledge on the role of diet, including fermented foods, in preventing or treating allergic diseases and asthma.
Collapse
|
10
|
Sharma AK, Davison S, Pafco B, Clayton JB, Rothman JM, McLennan MR, Cibot M, Fuh T, Vodicka R, Robinson CJ, Petrzelkova K, Gomez A. The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors. NPJ Biofilms Microbiomes 2022; 8:12. [PMID: 35301322 PMCID: PMC8930997 DOI: 10.1038/s41522-022-00274-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.
Collapse
Affiliation(s)
- Ashok K Sharma
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA.,Department of Gastroenterology, Inflammatory Bowel & Immunology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Sam Davison
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA.,Callitrichid Research Center (CRC, Marmoset Colony) at the University of Nebraska at Omaha, Omaha, NE, USA.,Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, USA.,New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Matthew R McLennan
- Department of Social Sciences, Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK.,Bulindi Chimpanzee & Community Project, Hoima, Uganda
| | - Marie Cibot
- Department of Social Sciences, Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK.,Bulindi Chimpanzee & Community Project, Hoima, Uganda.,Anicoon Vétérinaires, Ploemeur, France
| | - Terence Fuh
- WWF Central African Republic, Bayanga, Central African Republic
| | | | | | - Klara Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Brno, Czech Republic
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA. .,Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA.
| |
Collapse
|
11
|
Papadakis Z, Garcia-Retortillo S, Koutakis P. Effects of Acute Partial Sleep Deprivation and High-Intensity Interval Exercise on Postprandial Network Interactions. FRONTIERS IN NETWORK PHYSIOLOGY 2022; 2:869787. [PMID: 36926086 PMCID: PMC10013041 DOI: 10.3389/fnetp.2022.869787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
Introduction: High-intensity interval exercise (HIIE) is deemed effective for cardiovascular and autonomic nervous system (ANS) health-related benefits, while ANS disturbance increases the risk for cardiovascular disease (CVD). Postprandial lipemia and acute-partial sleep deprivation (APSD) are considered as CVD risk factors due to their respective changes in ANS. Exercising in the morning hours after APSD and have a high-fat breakfast afterwards may alter the interactions of the cardiovascular, autonomic regulation, and postprandial lipemic systems threatening individuals' health. This study examined postprandial network interactions between autonomic regulation through heart rate variability (HRV) and lipemia via low-density lipoprotein (LDL) cholesterol in response to APSD and HIIE. Methods: Fifteen apparently healthy and habitually good sleepers (age 31 ± 5.2 SD yrs) completed an acute bout of an isocaloric HIIE (in form of 3:2 work-to-rest ratio at 90 and 40% of VO2 reserve) after both a reference sleep (RSX) and 3-3.5 h of acute-partial sleep deprivation (SSX) conditions. HRV time and frequency domains and LDL were evaluated in six and seven time points surrounding sleep and exercise, respectively. To identify postprandial network interactions, we constructed one correlation analysis and one physiological network for each experimental condition. To quantify the interactions within the physiological networks, we also computed the number of links (i.e., number of significant correlations). Results: We observed an irruption of negative links (i.e., negative correlations) between HRV and LDL in the SSX physiological network compared to RSX. Discussion: We recognize that a correlation analysis does not constitute a true network analysis due to the absence of analysis of a time series of the original examined physiological variables. Nonetheless, the presence of negative links in SSX reflected the impact of sleep deprivation on the autonomic regulation and lipemia and, thus, revealed the inability of HIIE to remain cardioprotective under APSD. These findings underlie the need to further investigate the effects of APSD and HIIE on the interactions among physiological systems.
Collapse
Affiliation(s)
- Zacharias Papadakis
- Human Performance Laboratory, Department of Sport and Exercise Sciences, Barry University, Miami Shores, FL, United States
| | - Sergi Garcia-Retortillo
- Keck Laboratory for Network Physiology, Department of Physics, Boston University, Boston, MA, United States
| | - Panagiotis Koutakis
- Clinical Muscle Biology Laboratory, Department of Biology, Baylor University, Waco, TX, United States
| |
Collapse
|
12
|
The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Sci Rep 2021; 11:24017. [PMID: 34911987 PMCID: PMC8674285 DOI: 10.1038/s41598-021-03334-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.
Collapse
|
13
|
Bengtsson-Palme J, Jonsson V, Heß S. What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:15734-15743. [PMID: 34792330 PMCID: PMC8655980 DOI: 10.1021/acs.est.1c02977] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. It has been suggested that the environment constitutes an enormous recruitment ground for ARGs to pathogens, but its extent is practically unknown. We have constructed a model framework for resistance emergence and used available quantitative data on relevant processes to identify limiting steps in the appearance of ARGs in human pathogens. We found that in a majority of possible scenarios, the environment would only play a minor role in the emergence of novel ARGs. However, the uncertainty is enormous, highlighting an urgent need for more quantitative data. Specifically, more data is most needed on the fitness costs of ARG carriage, the degree of dispersal of resistant bacteria from the environment to humans, and the rates of mobilization and horizontal transfer of ARGs. This type of data is instrumental to determine which processes should be targeted for interventions to curb development and transmission of ARGs in the environment.
Collapse
Affiliation(s)
- Johan Bengtsson-Palme
- Department
of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden
- Centre
for Antibiotic Resistance Research (CARe) at University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Viktor Jonsson
- Integrated
Science Lab, Department of Physics, Umeå
University, SE-901 87 Umeå, Sweden
| | - Stefanie Heß
- Institute
of Microbiology, Technische Universität
Dresden, Zellescher Weg
20b, 01847 Dresden, Germany
| |
Collapse
|
14
|
Scaccia N, Vaz-Moreira I, Manaia CM. The risk of transmitting antibiotic resistance through endophytic bacteria. TRENDS IN PLANT SCIENCE 2021; 26:1213-1226. [PMID: 34593300 DOI: 10.1016/j.tplants.2021.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is a global human health threat distributed across humans, animals, plants, and the environment. Under the One-Health concept (humans, animals, and environment), the contamination of water bodies and soil by antibiotic-resistant bacteria cannot be dissociated from its potential transmission to humans. Edible plants can be colonized by a vast diversity of bacteria, representing an important link between the environment and humans in the One-Health triad. Based on multiple examples of bacterial groups that comprise endophytes reported in edible plants, and that have close phylogenetic proximity with human opportunistic pathogens, we argue that plants exposed to human-derived biological contamination may represent a path of transmission of antibiotic resistance to humans.
Collapse
Affiliation(s)
- Nazareno Scaccia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal.
| |
Collapse
|
15
|
Health effects and probiotic and prebiotic potential of Kombucha: A bibliometric and systematic review. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101332] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
16
|
Neuro-immune-metabolism: The tripod system of homeostasis. Immunol Lett 2021; 240:77-97. [PMID: 34655659 DOI: 10.1016/j.imlet.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/30/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022]
Abstract
Homeostatic regulation of cellular and molecular processes is essential for the efficient physiological functioning of body organs. It requires an intricate balance of several networks throughout the body, most notable being the nervous, immune and metabolic systems. Several studies have reported the interactions between neuro-immune, immune-metabolic and neuro-metabolic pathways. Current review aims to integrate the information and show that neuro, immune and metabolic systems form the triumvirate of homeostasis. It focuses on the cellular and molecular interactions occurring in the extremities and intestine, which are innervated by the peripheral nervous system and for the intestine in particular the enteric nervous system. While the interdependence of neuro-immune-metabolic pathways provides a fallback mechanism in case of disruption of homeostasis, in chronic pathologies of continued disequilibrium, the collapse of one system spreads to the other interacting networks as well. Current review illustrates this domino-effect using diabetes as the main example. Together, this review attempts to provide a holistic picture of the integrated network of neuro-immune-metabolism and attempts to broaden the outlook when devising a scientific study or a treatment strategy.
Collapse
|
17
|
Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
Collapse
Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | |
Collapse
|
18
|
Berding K, Vlckova K, Marx W, Schellekens H, Stanton C, Clarke G, Jacka F, Dinan TG, Cryan JF. Diet and the Microbiota-Gut-Brain Axis: Sowing the Seeds of Good Mental Health. Adv Nutr 2021; 12:1239-1285. [PMID: 33693453 PMCID: PMC8321864 DOI: 10.1093/advances/nmaa181] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the gut microbiota has emerged as a key component in regulating brain processes and behavior. Diet is one of the major factors involved in shaping the gut microbiota composition across the lifespan. However, whether and how diet can affect the brain via its effects on the microbiota is only now beginning to receive attention. Several mechanisms for gut-to-brain communication have been identified, including microbial metabolites, immune, neuronal, and metabolic pathways, some of which could be prone to dietary modulation. Animal studies investigating the potential of nutritional interventions on the microbiota-gut-brain axis have led to advancements in our understanding of the role of diet in this bidirectional communication. In this review, we summarize the current state of the literature triangulating diet, microbiota, and host behavior/brain processes and discuss potential underlying mechanisms. Additionally, determinants of the responsiveness to a dietary intervention and evidence for the microbiota as an underlying modulator of the effect of diet on brain health are outlined. In particular, we emphasize the understudied use of whole-dietary approaches in this endeavor and the need for greater evidence from clinical populations. While promising results are reported, additional data, specifically from clinical cohorts, are required to provide evidence-based recommendations for the development of microbiota-targeted, whole-dietary strategies to improve brain and mental health.
Collapse
Affiliation(s)
| | | | - Wolfgang Marx
- Deakin University, iMPACT – the Institute for Mental and Physical Health and Clinical Translation, Food & Mood Centre, School of Medicine, Barwon Health, Geelong, VIC,Australia
| | - Harriet Schellekens
- APC Microbiome Ireland, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - Felice Jacka
- Deakin University, iMPACT – the Institute for Mental and Physical Health and Clinical Translation, Food & Mood Centre, School of Medicine, Barwon Health, Geelong, VIC,Australia
- Centre for Adolescent Health, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Black Dog Institute, Randwick, NSW, Australia
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Douglas, QLD, Australia
| | - Timothy G Dinan
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| |
Collapse
|
19
|
Brame JE, Liddicoat C, Abbott CA, Breed MF. The potential of outdoor environments to supply beneficial butyrate-producing bacteria to humans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:146063. [PMID: 33684759 DOI: 10.1016/j.scitotenv.2021.146063] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Butyrate is an important mediator of human health and disease. The mechanisms of action of butyrate are becoming increasingly well-known. Many commensal bacteria that inhabit the human gut can synthesise butyrate, which is then absorbed into the human host. Simultaneously, several immune- and inflammatory-mediated diseases are being linked to insufficient exposure to beneficial microbes from our environment, including butyrate-producing bacteria. However, the role of outdoor environmental exposure to butyrate-producing bacteria remains poorly understood. Here we review the literature on the human exposure pathways to butyrate-producing bacteria, with a particular focus on outdoor environmental sources (e.g. associated with plants, plant-based residues, and soil), and the health implications of exposure to them. Emerging evidence suggests that environmental butyrate-producers may help supplement the human gut microbiota and represent an important component of the Biodiversity and Old Friends hypotheses. Improving our understanding of potential sources, precursors, and exposure pathways of environmental butyrate-producers that influence the gut microbiota and butyrate production offers promise to advance multiple disciplines of health and environmental science. We outline research priorities to address knowledge gaps in the outdoor environment-butyrate-health nexus and build knowledge of the potential pathways to help optimise exposure to human-beneficial butyrate-producing bacteria from the outdoor environment during childhood and adulthood.
Collapse
Affiliation(s)
- Joel E Brame
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia; School of Public Health, The University of Adelaide, SA 5005, Australia
| | - Catherine A Abbott
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| |
Collapse
|
20
|
Wongkaew M, Tinpovong B, Sringarm K, Leksawasdi N, Jantanasakulwong K, Rachtanapun P, Hanmoungjai P, Sommano SR. Crude Pectic Oligosaccharide Recovery from Thai Chok Anan Mango Peel Using Pectinolytic Enzyme Hydrolysis. Foods 2021; 10:627. [PMID: 33809517 PMCID: PMC7999440 DOI: 10.3390/foods10030627] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Pectin recovered from mango peel biomass can be used as a potential source for pectic oligosaccharide hydrolysate with excellent probiotic growth-enhancing performance and prebiotic potentials. Consequently, the objectives of the current study were to optimise the enzyme hydrolysis treatment of mango peel pectin (MPP) and to evaluate the pectic oligosaccharide effects of Lactobacillus reuteri DSM 17938 and Bifidobacterium animalis TISTR 2195. Mango of "chok anan" variety was chosen due to its excessive volume of biomass in processing and high pectin content. The optimal treatment for mango peel pectic oligosaccharide (MPOS) valorisation was 24 h of fermentation with 0.3% (v/v) pectinase. This condition provided small oligosaccharides with the molecular weight of 643 Da that demonstrated the highest score of prebiotic activity for both of B. animalis TISTR 2195 (7.76) and L. reuteri DSM 17938 (6.87). The major sugar compositions of the oligosaccharide were fructose (24.41% (w/w)) and glucose (19.52% (w/w)). For the simulation of prebiotic fermentation, B. animalis TISTR 2195 showed higher proliferation in 4% (w/v) of MPOS supplemented (8.92 log CFU/mL) than that of L. reuteri (8.53 CFU/mL) at 72 h of the fermentation time. The main short chain fatty acids (SCFAs) derived from MPOS were acetic acid and propionic acid. The highest value of total SCFA was achieved from the 4% (w/v) MPOS supplementation for both of B. animalis (68.57 mM) and L. reuteri (69.15 mM). The result of this study therefore conclusively advises that MPOS is a novel pectic oligosaccharide resource providing the opportunity for the sustainable development approach through utilising by-products from the fruit industry.
Collapse
Affiliation(s)
- Malaiporn Wongkaew
- Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand;
- Program of Food Production and Innovation, Faculty of Integrated Science and Technology, Rajamangala University of Technology Lanna, Chiang Mai 50300, Thailand;
- Plant Bioactive Compound Laboratory, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Bow Tinpovong
- Program of Food Production and Innovation, Faculty of Integrated Science and Technology, Rajamangala University of Technology Lanna, Chiang Mai 50300, Thailand;
| | - Korawan Sringarm
- Department of Animal and Aquatic Science, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), Chiang Mai University, Chiang Mai 50200, Thailand; (N.L.); (K.J.); (P.R.)
| | - Noppol Leksawasdi
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), Chiang Mai University, Chiang Mai 50200, Thailand; (N.L.); (K.J.); (P.R.)
- School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Kittisak Jantanasakulwong
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), Chiang Mai University, Chiang Mai 50200, Thailand; (N.L.); (K.J.); (P.R.)
- School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Pornchai Rachtanapun
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), Chiang Mai University, Chiang Mai 50200, Thailand; (N.L.); (K.J.); (P.R.)
- School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Prasert Hanmoungjai
- School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Sarana Rose Sommano
- Plant Bioactive Compound Laboratory, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), Chiang Mai University, Chiang Mai 50200, Thailand; (N.L.); (K.J.); (P.R.)
| |
Collapse
|
21
|
Michels KB, Willett WC, Vaidya R, Zhang X, Giovannucci E. Yogurt consumption and colorectal cancer incidence and mortality in the Nurses' Health Study and the Health Professionals Follow-Up Study. Am J Clin Nutr 2020; 112:1566-1575. [PMID: 33022694 PMCID: PMC7727484 DOI: 10.1093/ajcn/nqaa244] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Yogurt is a commonly consumed fermented food. Regular yogurt consumption may contribute to a favorable gut microbiome and gut health, but few epidemiologic studies have considered the relation between regular yogurt consumption and the incidence of and mortality from colorectal cancer. OBJECTIVES We used data from 2 large, prospective cohort studies, the Nurses' Health Study and the Health Professionals Follow-Up Study, to examine the role of yogurt consumption on colorectal cancer incidence and mortality. METHODS During 32 years of follow-up in 83,054 women (mean age at baseline, 45.7 years) and 26 years of follow-up in 43,269 men (mean age at baseline, 52.3 years), we documented a total of 2666 newly diagnosed cases of colorectal cancer in these cohorts. We modeled yogurt consumption at baseline and cumulatively updated it throughout follow-up. Results: Baseline yogurt consumption was associated with a reduced risk of colon cancer in age-adjusted analyses (P for trend < 0.001). Associations remained statistically significant after adjusting for potential confounders, including calcium and fiber intake (P for trend = 0.03), and were restricted to proximal colon cancer. The consumption of 1 + servings per week of yogurt at baseline, compared to no yogurt consumption, was associated with a multivariable HR of 0.84 (95% CI, 0.70-0.99; P trend = 0.04) for the proximal colon cancer incidence. Latency analyses suggested that the most important window of opportunity for regular yogurt consumption to prevent colorectal cancer was 16-20 years in the past. When yogurt consumption was cumulatively updated, associations attenuated and were no longer significant. No statistically significant inverse trend was observed between yogurt consumption and the colorectal cancer mortality. CONCLUSIONS In these large cohorts, the frequency of yogurt consumption was associated with a reduced risk of proximal colon cancer with a long latency period. No significant inverse trend was observed for colorectal cancer mortality.
Collapse
Affiliation(s)
- Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, California, USA
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | - Walter C Willett
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts,USA
| | - Rita Vaidya
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Xuehong Zhang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts,USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts,USA
| |
Collapse
|
22
|
Marco ML, Hill C, Hutkins R, Slavin J, Tancredi DJ, Merenstein D, Sanders ME. Should There Be a Recommended Daily Intake of Microbes? J Nutr 2020; 150:3061-3067. [PMID: 33269394 PMCID: PMC7726123 DOI: 10.1093/jn/nxaa323] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
The collective findings from human microbiome research, randomized controlled trials on specific microbes (i.e., probiotics), and associative studies of fermented dairy consumption provide evidence for the beneficial effects of the regular consumption of safe live microbes. To test the hypothesis that the inclusion of safe, live microbes in the diet supports and improves health, we propose assessment of the types and evidentiary quality of the data available on microbe intake, including the assembly and evaluation of evidence available from dietary databases. Such an analysis would help to identify gaps in the evidence needed to test this hypothesis, which can then be used to formulate and direct initiatives focused on prospective and randomized controlled trials on live microbe consumption. Outcomes will establish whether or not the evidence exists, or can be generated, to support the establishment of dietary recommendations for live microbes.
Collapse
Affiliation(s)
- Maria L Marco
- Department of Food Science & Technology, University of California, Davis, CA, USA
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Joanne Slavin
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Daniel J Tancredi
- Department of Pediatrics and Center for Healthcare Policy and Research, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Daniel Merenstein
- Department of Family Medicine, Georgetown University, Washington DC, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| |
Collapse
|
23
|
De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
Collapse
Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| |
Collapse
|
24
|
Johnson AJ, Zheng JJ, Kang JW, Saboe A, Knights D, Zivkovic AM. A Guide to Diet-Microbiome Study Design. Front Nutr 2020; 7:79. [PMID: 32596250 PMCID: PMC7303276 DOI: 10.3389/fnut.2020.00079] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Intense recent interest in understanding how the human gut microbiome influences health has kindled a concomitant interest in linking dietary choices to microbiome variation. Diet is known to be a driver of microbiome variation, and yet the precise mechanisms by which certain dietary components modulate the microbiome, and by which the microbiome produces byproducts and secondary metabolites from dietary components, are not well-understood. Interestingly, despite the influence of diet on the gut microbiome, the majority of microbiome studies published to date contain little or no analysis of dietary intake. Although an increasing number of microbiome studies are now collecting some form of dietary data or even performing diet interventions, there are no clear standards in the microbiome field for how to collect diet data or how to design a diet-microbiome study. In this article, we review the current practices in diet-microbiome analysis and study design and make several recommendations for best practices to provoke broader discussion in the field. We recommend that microbiome studies include multiple consecutive microbiome samples per study timepoint or phase and multiple days of dietary history prior to each microbiome sample whenever feasible. We find evidence that direct effects of diet on the microbiome are likely to be observable within days, while the length of an intervention required for observing microbiome-mediated effects on the host phenotype or host biomarkers, depending on the outcome, may be much longer, on the order of weeks or months. Finally, recent studies demonstrating that diet-microbiome interactions are personalized suggest that diet-microbiome studies should either include longitudinal sampling within individuals to identify personalized responses, or should include an adequate number of participants spanning a range of microbiome types to identify generalized responses.
Collapse
Affiliation(s)
- Abigail J Johnson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Jack Jingyuan Zheng
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Jea Woo Kang
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Anna Saboe
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Angela M Zivkovic
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| |
Collapse
|
25
|
Scaccia N, Vaz-Moreira I, Manaia CM. Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material. FEMS Microbiol Ecol 2020; 96:5815073. [PMID: 32239211 DOI: 10.1093/femsec/fiaa058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/27/2020] [Indexed: 01/11/2023] Open
Abstract
Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.
Collapse
Affiliation(s)
- Nazareno Scaccia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| |
Collapse
|
26
|
Harnessing Microbes for Sustainable Development: Food Fermentation as a Tool for Improving the Nutritional Quality of Alternative Protein Sources. Nutrients 2020; 12:nu12041020. [PMID: 32276384 PMCID: PMC7230334 DOI: 10.3390/nu12041020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/26/2020] [Accepted: 04/07/2020] [Indexed: 12/21/2022] Open
Abstract
In order to support the multiple levels of sustainable development, the nutritional quality of plant-based protein sources needs to be improved by food technological means. Microbial fermentation is an ancient food technology, utilizing dynamic populations of microorganisms and possessing a high potential to modify chemical composition and cell structures of plants and thus to remove undesirable compounds and to increase bioavailability of nutrients. In addition, fermentation can be used to improve food safety. In this review, the effects of fermentation on the protein digestibility and micronutrient availability in plant-derived raw materials are surveyed. The main focus is on the most important legume, cereal, and pseudocereal species (Cicer arietinum, Phaseolus vulgaris, Vicia faba, Lupinus angustifolius, Pisum sativum, Glycine max; Avena sativa, Secale cereale, Triticum aestivum, Triticum durum, Sorghum bicolor; and Chenopodium quinoa, respectively) of the agrifood sector. Furthermore, the current knowledge regarding the in vivo health effects of fermented foods is examined, and the critical points of fermentation technology from the health and food safety point of view are discussed.
Collapse
|
27
|
Gänzle MG. Food fermentations for improved digestibility of plant foods – an essential ex situ digestion step in agricultural societies? Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
28
|
Venter C, Eyerich S, Sarin T, Klatt KC. Nutrition and the Immune System: A Complicated Tango. Nutrients 2020; 12:nu12030818. [PMID: 32204518 PMCID: PMC7146186 DOI: 10.3390/nu12030818] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
Enthusiasm exists for the potential of diet to impact the immune system, prevent disease and its therapeutic potential. Herein, we describe the challenge to nutrition scientists in defining this relationship through case studies of diets and nutrients in the context of allergic and autoimmune diseases. Moderate-quality evidence exists from both human intervention and observational studies to suggest that diet and individual nutrients can influence systemic markers of immune function and inflammation; numerous challenges exist for demonstrating the impact of defined diets and nutrient interventions on clearly influencing immune-mediated-clinical disease endpoints. A growing body of evidence suggests that further consideration of dietary patterns, immune system and gut microbiome composition and function, and subsequent epigenetic modifications are needed to improve our understanding of diet–immune system interactions.
Collapse
Affiliation(s)
- Carina Venter
- Section of Allergy & Immunology, School of Medicine, University of Colorado Denver, Children’s Hospital Colorado, Anschutz Medical Campus, 13123 East 16th Avenue, Aurora, CO 80045, USA;
- Correspondence: ; Tel.: +1-720-777-6844
| | - Stefanie Eyerich
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrass 29, 80802 Munich, Germany;
| | - Tara Sarin
- Section of Allergy & Immunology, School of Medicine, University of Colorado Denver, Children’s Hospital Colorado, Anschutz Medical Campus, 13123 East 16th Avenue, Aurora, CO 80045, USA;
| | - Kevin C. Klatt
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA;
| |
Collapse
|
29
|
Venter C, Greenhawt M, Meyer RW, Agostoni C, Reese I, Toit G, Feeney M, Maslin K, Nwaru BI, Roduit C, Untersmayr E, Vlieg‐Boerstra B, Pali‐Schöll I, Roberts GC, Smith P, Akdis CA, Agache I, Ben‐Adallah M, Bischoff S, Frei R, Garn H, Grimshaw K, Hoffmann‐Sommergruber K, Lunjani N, Muraro A, Poulsen LK, Renz H, Sokolowska M, Stanton C, O'Mahony L. EAACI position paper on diet diversity in pregnancy, infancy and childhood: Novel concepts and implications for studies in allergy and asthma. Allergy 2020; 75:497-523. [PMID: 31520486 DOI: 10.1111/all.14051] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023]
Abstract
To fully understand the role of diet diversity on allergy outcomes and to set standards for conducting research in this field, the European Academy of Allergy and Clinical Immunology Task Force on Diet and Immunomodulation has systematically explored the association between diet diversity and allergy outcomes. In addition, a detailed narrative review of information on diet quality and diet patterns as they pertain to allergic outcomes is presented. Overall, we recommend that infants of any risk category for allergic disease should have a diverse diet, given no evidence of harm and some potential association of benefit in the prevention of particular allergic outcomes. In order to harmonize methods for future data collection and reporting, the task force members propose relevant definitions and important factors for consideration, when measuring diet diversity in the context of allergy. Consensus was achieved on practice points through the Delphi method. It is hoped that the definitions and considerations described herein will also enable better comparison of future studies and improve mechanistic studies and pathway analysis to understand how diet diversity modulates allergic outcomes.
Collapse
Affiliation(s)
- Carina Venter
- Section of Allergy and Immunology Children's Hospital Colorado University of Colorado Denver School of Medicine Aurora CO USA
| | - Matthew Greenhawt
- Section of Allergy and Immunology Children's Hospital Colorado University of Colorado Denver School of Medicine Aurora CO USA
| | | | - Carlo Agostoni
- Fondazione IRCCS Ca' Granda ‐ Ospedale Maggiore Policlinico Milano Italy
- Dipartimento di Scienze Cliniche e di Comunita Universita' degli Studi Milano Italy
| | - Imke Reese
- Dietary Counseling and Nutrition Therapy Centre Munich Germany
| | - George Toit
- Department of Paediatric Allergy Division of Asthma, Allergy and Lung Biology King's College London London UK
- Guy's & St Thomas' Hospital London UK
| | - Mary Feeney
- Department of Paediatric Allergy Division of Asthma, Allergy and Lung Biology King's College London London UK
- Guy's & St Thomas' Hospital London UK
| | | | - Bright I. Nwaru
- Institute of Medicine Krefting Research Centre University of Gothenburg Gothenburg Sweden
| | - Caroline Roduit
- University Children's Hospital Zurich Zurich Switzerland
- Christine Kühne‐Center for Allergy Research and Education Davos Switzerland
| | - Eva Untersmayr
- Institute for Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | | | - Isabella Pali‐Schöll
- Department of Nutrition and Dietetics Hanze University of Applied Sciences Groningen The Netherlands
- Comparative Medicine Messerli Research Institute of the University of Veterinary Medicine Vienna Medical University Vienna Vienna Austria
| | - Graham C. Roberts
- The David Hide Asthma and Allergy Research Centre St Mary’s Hospital Newport UK
- NIHR Biomedical Research Centre University Hospital Southampton NHS Foundation Trust Southampton UK
- Faculty of Medicine Clinical and Experimental Sciences Human Development in Health Academic Units University of Southampton Southampton UK
| | - Peter Smith
- School of Medicine Griffith University Southport QLD Australia
| | - Cezmi A. Akdis
- Christine Kühne‐Center for Allergy Research and Education Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | | | - Miriam Ben‐Adallah
- Section of Allergy and Immunology Children's Hospital Colorado University of Colorado Denver School of Medicine Aurora CO USA
| | - Stephan Bischoff
- Institute of Nutritional Medicine University of Hohenheim Stuttgart Germany
| | - Remo Frei
- Christine Kühne‐Center for Allergy Research and Education Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Holger Garn
- Philipps University of Marburg - Medical Faculty Institute of Laboratory Medicine and Pathobiochemistry Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL) Marburg Germany
| | - Kate Grimshaw
- Faculty of Medicine Experimental Sciences & Human Development in Health Academic Units University of Southampton Southampton UK
- Department of Dietetics Salford Royal Foundation Trust Salford UK
| | - Karin Hoffmann‐Sommergruber
- Institute for Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Nonhlanhla Lunjani
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
- University of Cape Town Cape Town South Africa
| | - Antonella Muraro
- Centro di Specializzazione Regionale per lo Studio e la Cura delle Allergie e delle Intolleranze Alimentari presso l'Azienda Ospedaliera Università di Padova Padova Italy
| | - Lars K. Poulsen
- Department of Skin and Allergy Diseases Allergy Clinic Copenhagen University Hospital at Gentofte Copenhagen Denmark
| | - Harald Renz
- Institute of Laboratory Medicine Universities of Giessen and Marburg Lung Center (UGMLC) German Center for Lung Research (DZL) Philipps Universität Marburg Marburg Germany
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | | | - Liam O'Mahony
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
- Department of Medicine and Microbiology APC Microbiome Ireland National University of Ireland Cork Ireland
| |
Collapse
|
30
|
Hauptmann AL, Paulová P, Castro-Mejía JL, Hansen LH, Sicheritz-Pontén T, Mulvad G, Nielsen DS. The microbial composition of dried fish prepared according to Greenlandic Inuit traditions and industrial counterparts. Food Microbiol 2020; 85:103305. [DOI: 10.1016/j.fm.2019.103305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/14/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023]
|
31
|
Host-adapted lactobacilli in food fermentations: impact of metabolic traits of host adapted lactobacilli on food quality and human health. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
32
|
Hauptmann AL, Paulová P, Hansen LH, Sicheritz-Pontén T, Mulvad G, Nielsen DS. Microbiota in foods from Inuit traditional hunting. PLoS One 2020; 15:e0227819. [PMID: 31935269 PMCID: PMC6959823 DOI: 10.1371/journal.pone.0227819] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/30/2019] [Indexed: 01/21/2023] Open
Abstract
The foods we eat contain microorganisms that we ingest alongside the food. Industrialized food systems offer great advantages from a safety point of view, but have also been accused of depleting the diversity of the human microbiota with negative implications for human health. In contrast, artisanal traditional foods are potential sources of a diverse food microbiota. Traditional foods of the Greenlandic Inuit are comprised of animal-sourced foods prepared in the natural environment and are often consumed raw. These foods, some of which are on the verge of extinction, have not previously been microbiologically characterized. We mapped the microbiota of foods stemming from traditional Inuit land-based hunting activities. The foods included in the current study are dried muskox and caribou meat, caribou rumen and intestinal content as well as larval parasites from caribou hides, all traditional Inuit foods. This study shows that traditional drying methods are efficient for limiting microbial growth through desiccation. The results also show the rumen content of the caribou to be a highly diverse source of microbes with potential for degradation of plants. Finally, a number of parasites were shown to be included in the biodiversity of the assessed traditional foods. Taken together, the results map out a diverse source of ingested microbes and parasites that originate from the natural environment. These results have implications for understanding the nature-sourced traditional Inuit diet, which is in contrast to current day diet recommendations as well as modern industrialized food systems.
Collapse
Affiliation(s)
- Aviaja L. Hauptmann
- Greenland Center for Health Research, Ilisimatusarfik—University of Greenland, Nuuk, Greenland
- The Greenland Institute of Natural Resources, Nuuk, Greenland
- * E-mail:
| | - Petronela Paulová
- Department of Food Science, The University of Copenhagen, Frederiksberg, Denmark
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Thomas Sicheritz-Pontén
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Kedah, Malaysia
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gert Mulvad
- Greenland Center for Health Research, Ilisimatusarfik—University of Greenland, Nuuk, Greenland
| | - Dennis S. Nielsen
- Department of Food Science, The University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
33
|
Bacterial Community Sequences of Submerged Aquatic Vegetation in the Potomac River. Microbiol Resour Announc 2020; 9:9/1/e01175-19. [PMID: 31896632 PMCID: PMC6940284 DOI: 10.1128/mra.01175-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Here, we report results from PCR and sequencing of bacterial 16S rRNA genes from leaf and root surfaces from nine submerged aquatic vegetation (SAV) samples comprising five species. Samples were from four sites along the Potomac River. Here, we report results from PCR and sequencing of bacterial 16S rRNA genes from leaf and root surfaces from nine submerged aquatic vegetation (SAV) samples comprising five species. Samples were from four sites along the Potomac River.
Collapse
|
34
|
Bold J, Harris M, Fellows L, Chouchane M. Nutrition, the digestive system and immunity in COVID-19 infection. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:331-340. [PMID: 33244375 PMCID: PMC7682975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 07/18/2020] [Indexed: 11/01/2022]
Abstract
The current review aimed to synthesize the literature on the complex relationship between food consumption and nutritional status as well as the digestive system in order to examine the relationship between immunity and potential responses to COVID-19 infection. The goal is to help inform the many healthcare professionals working with COVID-19 patients. A literature search was performed on PubMed, Scopus, and EMBASE databases. Hand searches were also undertaken using Google and reference lists to identify recent evidence. Studies were critically appraised, and the findings were analyzed by narrative synthesis. Nutritional status can impact immunity in several ways, including affecting susceptibility to infection, severity of disease, and recovery time, and is therefore a significant consideration in the management of COVID-19. COVID-19 can also impact digestive function, which can further impact nutritional status. The role of Vitamin D deficiency in vulnerability to severe respiratory infections, including COVID-19, has been recognized, and it may have a role in treatment where deficiency is indicated. Healthcare professionals should be aware that obesity may be accompanied by micronutrient malnutrition including vitamin D deficiency and alterations in the microbiome and inflammatory responses, which can further impact immunity and disease severity. Multidisciplinary team-work is recommended in the management of patients with COVID-19, and approaches should include a consideration of nutritional status (both macronutrients and micronutrients), body weight, and gastrointestinal signs and symptom.
Collapse
Affiliation(s)
- Justine Bold
- School of Allied Health & Community, University of Worcester, Worcester, WR2 6AJ, UK
- Centre for Medical Education, Medical School, Cardiff University, Cardiff, CF14 4YS, UK
| | - Miranda Harris
- School of Allied Health & Community, University of Worcester, Worcester, WR2 6AJ, UK
| | - Lindsey Fellows
- School of Allied Health & Community, University of Worcester, Worcester, WR2 6AJ, UK
| | - Manal Chouchane
- School of Allied Health & Community, University of Worcester, Worcester, WR2 6AJ, UK
| |
Collapse
|
35
|
Hellweger FL, Vick C, Rückbeil F, Bucci V. Fresh Ideas Bloom in Gut Healthcare to Cross-Fertilize Lake Management. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14099-14112. [PMID: 31647664 DOI: 10.1021/acs.est.9b04218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Harmful bacteria may be the most significant threat to human gut and lake ecosystem health, and they are often managed using similar tools, like poisoning with antibiotics or algicides. Out-of-the-box thinking in human microbiome engineering is leading to novel methods, like engineering bacteria to kill pathogens, "persuade" them not to produce toxins, or "mop up" their toxins. The bacterial agent can be given a competitive edge via an exclusive nutrient, and they can be engineered to commit suicide once their work is done. Viruses can kill pathogens with specific DNA sequences or knock out their antibiotic resistance genes using CRISPR technology. Some of these ideas may work for lakes. We critically review novel methods for managing harmful bacteria in the gut from the perspective of managing toxic cyanobacteria in lakes, and discuss practical aspects such as modifying bacteria using genetic engineering or directed evolution, mass culturing and controlling the agents. A key knowledge gap is in the ecology of strains, like toxigenic vs nontoxigenic Microcystis, including allelopathic and Black Queen interactions. Some of the "gut methods" may have future potential for lakes, but there presently is no substitute for established management approaches, including reducing N and P nutrient inputs, and mitigating climate change.
Collapse
Affiliation(s)
- Ferdi L Hellweger
- Water Quality Engineering , Technical University of Berlin , Berlin 10623 , Germany
| | - Carsten Vick
- Water Quality Engineering , Technical University of Berlin , Berlin 10623 , Germany
| | - Fiona Rückbeil
- Water Quality Engineering , Technical University of Berlin , Berlin 10623 , Germany
| | - Vanni Bucci
- Department of Bioengineering , University of Massachusetts Dartmouth , North Dartmouth , Massachusetts 02747 , United States
| |
Collapse
|
36
|
Abstract
The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.
Collapse
Affiliation(s)
- Wiley Barton
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.,APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.,VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland
| | - Orla O'Sullivan
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.,APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.,VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland
| | - Paul D Cotter
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.,APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.,VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland
| |
Collapse
|
37
|
Gómez-Gallego C, Gueimonde M, Salminen S. The role of yogurt in food-based dietary guidelines. Nutr Rev 2019; 76:29-39. [PMID: 30452698 DOI: 10.1093/nutrit/nuy059] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the modern food technology era, one of the aims of food safety and quality is to eliminate or reduce the number of microorganisms in food. This may now be changing. In particular, the importance of live microorganisms as beneficial food constituents is now being recognized. Microorganisms present in food that contribute to the human diet include not only viable bacteria but also metabolites and bioactive components. Yogurt is one of the most biologically active foods consumed by humans. It is an excellent source of proteins, vitamins, and minerals. Additionally, the nutritional value is especially high relative to cost. Potential nutritional benefits are also associated with the ingestion of the bacteria that are ordinarily present at the time of consumption. Thus, yogurt serves as a major source of live bacteria in the human diet, as well as a delivery vehicle for added probiotic bacteria. Yogurt may provide a simple and affordable solution for enhancing the nutritional value of the diet, including the intake of live bacteria and their metabolites. A further benefit may be obtained when yogurt is used as a carrier for specific probiotic bacteria and/or prebiotic compounds. These factors suggest that yogurt could have a more visible role in food-based dietary guidelines.
Collapse
Affiliation(s)
- Carlos Gómez-Gallego
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Miguel Gueimonde
- Instituto de Productos Lácteos de Asturias (IPLA), Spanish National Research Council (CSIC), Villaviciosa, Spain
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| |
Collapse
|
38
|
Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria. mSphere 2019; 4:4/1/e00043-19. [PMID: 30787117 PMCID: PMC6382968 DOI: 10.1128/msphere.00043-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with “live rocks” through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment. Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate the hypotheses that newly established aquaria show clear microbial successional patterns over time and that common marine aquarium-conditioning practices, such as the addition of ocean-derived “live rocks” (defined as any “dead coral skeleton covered with crustose coralline algae” transferred into an aquarium from open ocean habitats) impact the diversity of microbial populations as well as nitrogen cycling in aquaria. We collected water chemistry data alongside water and sediment samples from two independent and newly established saltwater aquaria over a 3-month period. Microbial communities in samples were assessed by DNA extraction, amplification of the 16S rRNA gene, and Illumina MiSeq sequencing. Our results showed clear and replicable patterns of community succession in both aquaria, with the existence of multiple stable states for aquarium microbial assemblages. Notably, our results show that changes in aquarium microbial communities do not always correlate with water chemistry measurements and that operational taxonomic unit (OTU)-level patterns relevant to nitrogen cycling were not reported as statistically significant. Overall, our results demonstrate that aquarium perturbations have a substantial impact on microbial community profiles of aquarium water and sediment and that the addition of live rocks improves nutrient cycling by shifting aquarium communities toward a more typical saltwater assemblage of microbial taxa. IMPORTANCE Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with “live rocks” through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment.
Collapse
|
39
|
Cream Cheese-Derived Lactococcus chungangensis CAU 28 Modulates the Gut Microbiota and Alleviates Atopic Dermatitis in BALB/c Mice. Sci Rep 2019; 9:446. [PMID: 30679532 PMCID: PMC6345912 DOI: 10.1038/s41598-018-36864-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/27/2018] [Indexed: 12/26/2022] Open
Abstract
Atopic dermatitis (AD) has a drastic impact on human health owing to complex skin, gut microbiota, and immune responses. Some lactic acid bacteria (LAB) are effective in ameliorating AD; however, the alleviative effects of dairy products derived from these LAB remain unclear. In this study, the efficacies of Lactococcus chungangensis CAU 28 (CAU 28) cream cheese and L. chungangensis CAU 28 dry cells were evaluated for treating AD in an AD mouse model. Overall, CAU 28 cream cheese administration was more effective against AD than L. chungangensis CAU 28 dry cells. Faeces from CAU 28 cream cheese-administered mice had increased short chain fatty acid, butyrate, acetate, and lactic acid levels, as well as butyrate-producing bacteria, including Akkermansia, Bacteroides, Lactobacillus, and Ruminococcus. Furthermore, oral CAU 28 cream cheese administration resulted in regulatory T cell (Treg)-mediated suppression of T helper type 2 (Th2) immune responses in serum and mRNA expression levels in the ileum. Oral CAU 28 cream cheese further reduced IgE levels, in addition to eosinophil and mast cell numbers. Therefore, CAU 28 cream cheese administration induced a coordinated immune response involving short-chain fatty acids and gut microbiota, indicating its potential for use as a supplement for AD mitigation.
Collapse
|
40
|
Kõiv V, Arbo K, Maiväli Ü, Kisand V, Roosaare M, Remm M, Tenson T. Endophytic bacterial communities in peels and pulp of five root vegetables. PLoS One 2019; 14:e0210542. [PMID: 30633764 PMCID: PMC6329509 DOI: 10.1371/journal.pone.0210542] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022] Open
Abstract
Plants contain endophytic bacteria, whose communities both influence plant growth and can be an important source of probiotics. Here we used deep sequencing of a 16S rRNA gene fragment and bacterial cultivation to independently characterize the microbiomes of five plant species from divergent taxonomic orders—potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), neep (Brassica napus spp. napobrassica), and topinambur (Helianthus tuberosus). We found that both species richness and diversity tend to be higher in the peel, where Alphaproteobacteria and Actinobacteria dominate, while Gammaproteobacteria and Firmicutes dominate in the pulp. A statistical analysis revealed that the main characteristic features of the microbiomes of plant species originate from the peel microbiomes. Topinambur pulp displayed an interesting characteristic feature: it contained up to 108 CFUs of lactic acid bacteria, suggesting its use as a source of probiotic bacteria. We also detected Listeria sp., in topinambur pulps, however, the 16S rRNA gene fragment is unable to distinguish between pathogenic versus non-pathogenic species, so the evaluation of this potential health risk is left to a future study.
Collapse
Affiliation(s)
- Viia Kõiv
- Institute of Technology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Krõõt Arbo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülo Maiväli
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Märt Roosaare
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| |
Collapse
|
41
|
Lavefve L, Marasini D, Carbonero F. Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 87:147-185. [PMID: 30678814 DOI: 10.1016/bs.afnr.2018.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fermented foods are currently experiencing a re-discovery, largely driven by numerous health benefits claims. While fermented dairy, beer, and wine (and other alcoholic fermented beverages) have been the subject of intensive research, other plant-based fermented foods that are in some case widely consumed (kimchi/sauerkraut, pickles, kombucha) have received less scientific attention. In this chapter, the current knowledge on the microbiology and potential health benefits of such plant-based fermented foods are presented. Kimchi is the most studied, characterized by primarily acidic fermentation by lactic acid bacteria. Anti-obesity and anti-hypertension properties have been reported for kimchi and other pickled vegetables. Kombucha is the most popular non-alcoholic fermented drink. Kombucha's microbiology is remarkable as it involves all fermenters described in known fermented foods: lactic acid bacteria, acetic acid bacteria, fungi, and yeasts. While kombucha is often hyped as a "super-food," only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. The mode of action that has been studied and demonstrated the most is the probiotic one. However, it can be expected that fermentation metabolites may be prebiotic, or influence host health directly. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.
Collapse
Affiliation(s)
- Laura Lavefve
- Department of Food Science and Center for Human Nutrition, University of Arkansas, Fayetteville, AR, United States; Direction des Etudes Et Prestations (DEEP), Institut Polytechnique UniLaSalle, Beauvais, France
| | - Daya Marasini
- Department of Food Science and Center for Human Nutrition, University of Arkansas, Fayetteville, AR, United States
| | - Franck Carbonero
- Department of Food Science and Center for Human Nutrition, University of Arkansas, Fayetteville, AR, United States.
| |
Collapse
|
42
|
Kok CR, Hutkins R. Yogurt and other fermented foods as sources of health-promoting bacteria. Nutr Rev 2018; 76:4-15. [DOI: 10.1093/nutrit/nuy056] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Car Reen Kok
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
| |
Collapse
|
43
|
Hird SM, Ganz H, Eisen JA, Boyce WM. The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status. mSphere 2018; 3:e00382-18. [PMID: 30355662 PMCID: PMC6200988 DOI: 10.1128/msphere.00382-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/26/2018] [Indexed: 02/08/2023] Open
Abstract
Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent "flu-like" microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.
Collapse
Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Holly Ganz
- AnimalBiome, Oakland, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, Davis, California, USA
| | - Walter M Boyce
- Pathology, Microbiology and Immunology, University of California, Davis, Davis, California, USA
| |
Collapse
|
44
|
Horng KR, Ganz HH, Eisen JA, Marks SL. Effects of preservation method on canine ( Canis lupus familiaris) fecal microbiota. PeerJ 2018; 6:e4827. [PMID: 29844978 PMCID: PMC5970549 DOI: 10.7717/peerj.4827] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.
Collapse
Affiliation(s)
- Katti R Horng
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America.,William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States of America
| | - Holly H Ganz
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States of America.,AnimalBiome, Inc., Oakland, CA, United States of America
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States of America
| | - Stanley L Marks
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States of America
| |
Collapse
|
45
|
Bortoluzzi C, Pedroso AA, Mallo JJ, Puyalto M, Kim WK, Applegate TJ. Sodium butyrate improved performance while modulating the cecal microbiota and regulating the expression of intestinal immune-related genes of broiler chickens. Poult Sci 2018; 96:3981-3993. [PMID: 29050425 DOI: 10.3382/ps/pex218] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022] Open
Abstract
This study evaluated the effect of sodium butyrate (SB) on performance, expression of immune-related genes in the cecal tonsils, and cecal microbiota of broiler chickens when dietary energy and amino acids concentrations were reduced. Day-old male Ross 708 broiler chicks were fed dietary treatments in a 3 × 2 factorial design (8 pens per treatment) with 3 dietary formulations (control diet; reduction of 2.3% of amino acids and 60 kcal/kg; and reduction of 4.6% of amino acids and 120 kcal/kg) with or without the inclusion of 0.1% of SB. Feed intake (FI), body weight gain (BW gain), and feed conversion ratio (FCR) were recorded until 28 d of age. From 14 to 28 d, there was an interaction of nutrient density by SB (P = 0.003) wherein BW gain of birds fed SB was impaired less by the energy/amino acids reduction than unsupplemented birds. A similar result was obtained from 1 to 28 d (P = 0.004). No interaction (P < 0.05) between nutrient density by SB was observed for FCR. Nutritional density of the diets and SB modified the structure, composition, and predicted function of the cecal microbiota. The nutritionally reduced diet altered the imputed function performed by the microbiota and the SB supplementation reduced these variations, keeping the microbial function similar to that observed in chickens fed a control diet. The frequency of bacterial species presenting the butyryl-CoA: acetate CoA-transferase gene increased in the microbiota of chickens fed a nutritionally reduced diet without SB supplementation, and was not changed by nutrient density of the diet when supplemented with SB (interaction; P = 0.01). SB modulated the expression of immune related genes in the cecal tonsils; wherein SB upregulated the expression of A20 in broilers fed control diets (P < 0.05) and increased IL-6 expression (P < 0.05). These results show that SB had positive effects on the productive performance of broilers fed nutritionally reduced diets, partially by modulating the cecal microbiota and exerting immune-modulatory effects.
Collapse
Affiliation(s)
- C Bortoluzzi
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907.,Department of Poultry Science, University of Georgia, Athens, GA, 30602
| | | | | | | | - W K Kim
- Department of Poultry Science, University of Georgia, Athens, GA, 30602
| | - T J Applegate
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907.,Department of Poultry Science, University of Georgia, Athens, GA, 30602
| |
Collapse
|
46
|
Kohl KD. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology. Integr Comp Biol 2018; 57:674-681. [PMID: 28985331 DOI: 10.1093/icb/icx013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields.
Collapse
Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| |
Collapse
|
47
|
Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen JA. Characterization of shifts of koala ( Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ 2018; 6:e4452. [PMID: 29576947 PMCID: PMC5853612 DOI: 10.7717/peerj.4452] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 02/14/2018] [Indexed: 01/01/2023] Open
Abstract
Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities.
Collapse
Affiliation(s)
| | - Ladan Doroud
- Department of Computer Science, University of California, Davis, CA, United States of America
| | - Alana J Firl
- Genome Center, University of California, Davis, CA, United States of America
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, United States of America
| |
Collapse
|
48
|
Venter C, Groetch M, Netting M, Meyer R. A patient-specific approach to develop an exclusion diet to manage food allergy in infants and children. Clin Exp Allergy 2018; 48:121-137. [DOI: 10.1111/cea.13087] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022]
Affiliation(s)
- C. Venter
- Children's Hospital Colorado; University of Colorado; Aurora CO USA
| | - M. Groetch
- Icahn School of Medicine at Mount Sinai; Jaffe Food Allergy Institute; New York NY USA
| | - M. Netting
- Healthy Mothers Babies and Children's Theme; South Australian Health & Medical Research Institute; Adelaide SA Australia
- Discipline of Paediatrics; School of Medicine; University of Adelaide; Adelaide SA Australia
- Nutrition Department; Women's and Children's Health Network; Adelaide SA Australia
| | - R. Meyer
- Department Paediatrics; Imperial College; London UK
| |
Collapse
|
49
|
Kohl KD, Dearing MD, Bordenstein SR. Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract. Mol Ecol 2017; 27:1874-1883. [PMID: 29230893 DOI: 10.1111/mec.14460] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023]
Abstract
Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates, it has only been investigated using samples from faeces or the distal colon. Here, we collected the contents of five gut regions from seven rodent species and inventoried the bacterial communities by sequencing the 16S rRNA gene. We investigated how community structures varied across gut regions and whether the pattern of phylosymbiosis was present along the length of the gut. Gut communities varied by host species and gut region, with Oscillospira and Ruminococcus being more abundant in the stomach and hindgut regions. Gut microbial communities were highly distinguishable by host species across all gut regions, with the strength of the discrimination increasing along the length of the gut. Last, the pattern of phylosymbiosis was found in all five gut regions, as well as faeces. Aspects of the gut environment, such as oxygen levels, production of antimicrobials or other factors, may shift microbial communities across gut regions. However, regardless of these differences, host species maintain distinguishable, phylosymbiotic assemblages of microbes that may have functional impacts for the host.
Collapse
Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| |
Collapse
|
50
|
You X, Einson JE, Lopez-Pena CL, Song M, Xiao H, McClements DJ, Sela DA. Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice. NPJ Sci Food 2017; 1:8. [PMID: 31304250 PMCID: PMC6550245 DOI: 10.1038/s41538-017-0006-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 06/20/2017] [Accepted: 07/11/2017] [Indexed: 12/19/2022] Open
Abstract
Diet is an important factor influencing the composition and function of the gut microbiome, but the effect of antimicrobial agents present within foods is currently not understood. In this study, we investigated the effect of the food-grade cationic antimicrobial ε-polylysine on the gut microbiome structure and predicted metagenomic function in a mouse model. The relative abundances of predominant phyla and genera, as well as the overall community structure, were perturbed in response to the incorporation of dietary ε-polylysine. Unexpectedly, this modification to the gut microbiome was experienced transiently and resolved to the initial basal composition at the final sampling point. In addition, a differential non-random assembly was observed in the microbiomes characterized from male and female co-housed animals, although their perturbation trajectories in response to diet remain consistent. In conclusion, antimicrobial ε-polylysine incorporated into food systems transiently alters gut microbial communities in mice, as well as their predicted function. This indicates a dynamic but resilient microbiome that adapts to microbial-active dietary components.
Collapse
Affiliation(s)
- Xiaomeng You
- Department of Food Science, University of Massachusetts, Amherst, MA 01003 USA
| | - Jonah E. Einson
- Department of Food Science, University of Massachusetts, Amherst, MA 01003 USA
- Commonwealth Honors College, University of Massachusetts, Amherst, MA 01003 USA
| | - Cynthia Lyliam Lopez-Pena
- Department of Food Science, University of Massachusetts, Amherst, MA 01003 USA
- Nestlé Nutrition, 445 State St., Fremont, MI 49413 USA
| | - Mingyue Song
- Department of Food Science, University of Massachusetts, Amherst, MA 01003 USA
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA 01003 USA
| | | | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA 01003 USA
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003 USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA 01655 USA
| |
Collapse
|