{"type": "FeatureCollection", "features": [{"id": "10.1002/jsfa.11205", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:14:06Z", "type": "Journal Article", "created": "2021-03-12", "title": "A novel ammoniation treatment of barley as a strategy to optimize rumen pH, feed degradability and microbial protein synthesis", "description": "AbstractBACKGROUND<p>Meeting the energy and nitrogen (N) requirements of high\uffe2\uff80\uff90performing ruminants at the same time as avoiding digestive disturbances (i.e. rumen acidosis) is a key priority in ruminant nutrition. The present study evaluated the effect of a cereal ammoniation treatment, in which barley grains are combined with urea and enzymes that catalyze the conversion of urea to ammonia to optimize rumen function. Twelve rumen cannulated sheep were randomly divided into two groups and fed a diet containing 60% of ammoniated barley (AMM) or untreated barley supplemented with urea (CTL) to investigate the impact on rumen fermentation and feed utilization.</p>RESULTS<p>AMM had higher total N content and effective rumen degradable N than untreated barely. AMM sheep had a consistently higher rumen pH throughout the day (6.31 versus 6.03) and tended to have a lower post\uffe2\uff80\uff90prandial ammonia peak and higher acetate molar proportion (+5.1%) than CTL sheep. The rumen environment in AMM sheep favored the colonization and utilization of agro\uffe2\uff80\uff90industrial by\uffe2\uff80\uff90products (i.e. orange pulp) by the rumen microbes leading to a higher feed degradability. AMM sheep also had higher total tract apparent N digestibility (+21.7%) and urinary excretion of purine derivatives (+34%), suggesting a higher N uptake and microbial protein synthesis than CTL sheep.</p>CONCLUSION<p>The inclusion of AMM in the diet of ruminants represents a valid strategy for maintaining rumen pH within a physiological range and improving N utilization by the rumen microbes, which could have positive effects on the health and productivity of animals in intensive production systems. These findings warrant further studies under conventional farm conditions. \uffc2\uffa9 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.</p>", "keywords": ["2. Zero hunger", "Rumen", "Sheep", "Bacteria", "Food Handling", "0402 animal and dairy science", "Hordeum", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Animal Feed", "Diet", "Gastrointestinal Microbiome", "Bacterial Proteins", "Ammonia", "Barley", "Rumen fermentation", "Animals", "Urea", "Ammoniation", "Digestion", "Feed utilization", "Research Articles"]}, "links": [{"href": "https://eprints.gla.ac.uk/235892/1/235892.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.11205"}, {"href": "https://doi.org/10.1002/jsfa.11205"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.11205", "name": "item", "description": "10.1002/jsfa.11205", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.11205"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-24T00:00:00Z"}}, {"id": "10.1007/s00018-021-04080-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:14:20Z", "type": "Journal Article", "created": "2022-01-19", "title": "Outlook on next\u2010generation probiotics from the human gut", "description": "Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored reservoir of potentially beneficial microbes. For this reason, academic and industrial research is focused on identifying and testing novel microbial strains of gut origin for the development of next-generation probiotics. Although several of these are promising for the prevention and treatment of many chronic diseases, studies on human subjects are still scarce and approval from regulatory agencies is, therefore, rare. In addition, some issues need to be overcome before implementing their wide application on the market, such as the best methods for cultivation and storage of these oxygen-sensitive taxa. This review summarizes the most recent evidence related to NGPs and provides an outlook to the main issues that still limit their wide employment.", "keywords": ["0301 basic medicine", "Gut microbiome", "Clostridiales", "0303 health sciences", "Bacteria", "Faecalibacterium prausnitzii", "Probiotics", "Next-generation probiotics", "Prevotella", "Akkermansia", "Bacterial Physiological Phenomena", "Gastrointestinal Microbiome", "3. Good health", "03 medical and health sciences", "Akkermansia muciniphila; Faecalibacterium prausnitzii; Gut microbiome; Live biotherapeutics; Next-generation probiotics; Prevotella copri", "Live biotherapeutics", "Dysbiosis", "Humans", "Prevotella copri", "Akkermansia muciniphila"], "contacts": [{"organization": "De Filippis F., Esposito A., Ercolini D.,", "roles": ["creator"]}]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/868940/2/CMLS%2c2022_NGP.pdf"}, {"href": "https://link.springer.com/content/pdf/10.1007/s00018-021-04080-6.pdf"}, {"href": "https://doi.org/10.1007/s00018-021-04080-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cellular%20and%20Molecular%20Life%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00018-021-04080-6", "name": "item", "description": "10.1007/s00018-021-04080-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00018-021-04080-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-19T00:00:00Z"}}, {"id": "10.1016/j.cub.2020.09.063", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:49Z", "type": "Journal Article", "created": "2020-10-15", "title": "Newly explored\u00a0Faecalibacterium\u00a0diversity is connected to age, lifestyle, geography, and disease.", "description": "Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.", "keywords": ["Adult", "0301 basic medicine", "pangenome", "Adolescent", "gut microbiome", "Datasets as Topic", "General Biochemistry", " Genetics and Molecular Biology", "Innovation action", "Feces", "03 medical and health sciences", "Animals", "Humans", "biotherapeutics", "European Commission", "Child", "Life Style", "Faecalibacterium", "Aged", "Aurora Universities Network", "Horizon 2020", "0303 health sciences", "EC", "Geography", "Faecalibacterium prausnitzii", "H2020", "Age Factors", "Infant", "Middle Aged", "Gastrointestinal Microbiome", "Faecalibacterium prausnitzii", " gut microbiome", " strain diversity", " pangenome", " novel probiotics", " biotherapeutics", "Child", " Preschool", "novel probiotics", "Dysbiosis", "Macaca", "Metagenome", "strain diversity", "Metagenomics", "General Agricultural and Biological Sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/819607/1/PIIS0960982220314330.pdf"}, {"href": "https://doi.org/10.1016/j.cub.2020.09.063"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cub.2020.09.063", "name": "item", "description": "10.1016/j.cub.2020.09.063", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cub.2020.09.063"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.172175", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:42Z", "type": "Journal Article", "created": "2024-04-02", "title": "Exploring the potential of earthworm gut bacteria for plastic degradation", "description": "The use of plastic mulch films in agriculture leads to the inevitable accumulation of plastic debris in soils. Here, we explored the potential of earthworm gut-inhabiting bacterial strains (Mycobacterium vanbaalenii (MV), Rhodococcus jostii (RJ), Streptomyces fulvissimus (SF), Bacillus simplex (BS), and Sporosarcina globispora (SG) to degrade plastic films (\u2300\u00a0=\u00a015\u00a0mm) made from commonly used polymers: low-density polyethylene film (LDPE-f), polylactic acid (PLA-f), polybutylene adipate terephthalate film (PBAT-f), and a commercial biodegradable mulch film, Bionov-B\u00ae (composed of Mater-Bi, a feedstock with PBAT, PLA and other chemical compounds). A 180-day experiment was conducted at room temperature (x\u0304 =19.4\u00a0\u00b0C) for different strain-plastic combinations under a low carbon media (0.1\u00d7 tryptic soy broth). Results showed that the tested strain-plastic combinations did not facilitate the degradation of LDPE-f (treated with RJ and SF), PBAT-f (treated with BS and SG), and Bionov-B (treated with BS, MV, and SG). However, incubating PLA-f with SF triggered a reduction in the molecular weights and an increase in crystallinity. Therefore, we used PLA-f as model plastic to study the influence of temperature ('room temperature' & '30\u00a0\u00b0C'), carbon source ('carbon-free' & 'low carbon supply'), and strain interactions ('single strains' & 'strain mixtures') on PLA degradation. SF and SF\u00a0+\u00a0RJ treatments significantly fostered PLA degradation under 30\u00a0\u00b0C in a low-carbon media. PLA-f did not show any degradation in carbon-free media treatments. The competition between different strains in the same system likely hindered the performance of PLA-degrading strains. A positive correlation between the final pH of culture media and PLA-f weight loss was observed, which might reflect the pH-dependent hydrolysis mechanism of PLA. Our results situate SF and its co-culture with RJ strains as possible accelerators of PLA degradation in temperatures below PLA glass transition temperature (Tg). Further studies are needed to test the bioremediation feasibility in soils.", "keywords": ["0301 basic medicine", "Bacteria", "ddc:550", "Polyesters", "01 natural sciences", "6. Clean water", "Gastrointestinal Microbiome", "03 medical and health sciences", "Biodegradation", " Environmental", "Life Science", "Animals", "Soil Pollutants", "Oligochaeta", "Plastics", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.172175"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2024.172175", "name": "item", "description": "10.1016/j.scitotenv.2024.172175", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.172175"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-06-01T00:00:00Z"}}, {"id": "10.1038/s41467-020-16438-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:34Z", "type": "Journal Article", "created": "2020-05-25", "title": "Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome", "description": "Abstract<p>Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.</p>", "keywords": ["Primates", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Science", "Probiotics", "Q", "gut microbiome", "Article", "Gastrointestinal Microbiome", "lactic acid bacteria", "Lactococcus lactis", "03 medical and health sciences", "Lactobacillales", "Databases", " Genetic", "Food Microbiology", "Animals", "Humans", "Metagenome", "Streptococcus thermophilus", "Fermented Foods", "[PHYS.ASTR] Physics [physics]/Astrophysics [astro-ph]", "Life Style", "genome analysis"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/269813/1/s41467-020-16438-8.pdf"}, {"href": "https://www.iris.unina.it/bitstream/11588/811717/2/NatComm%2c2020_LABfoodgut.pdf"}, {"href": "https://www.nature.com/articles/s41467-020-16438-8.pdf"}, {"href": "https://doi.org/10.1038/s41467-020-16438-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-020-16438-8", "name": "item", "description": "10.1038/s41467-020-16438-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-020-16438-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-25T00:00:00Z"}}, {"id": "10.1038/s41467-024-51398-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:34Z", "type": "Journal Article", "created": "2024-08-13", "title": "Insights into the ecology of the infant gut plasmidome", "description": "Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate the gut microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow to understand the impact of plasmids on the gut microbiome. We create a plasmid phylogenetic tree, devise a method for assigning plasmid hosts, and examine potential plasmid transfer networks. Our research discovers a wide variety of previously unidentified plasmid sequences, indicating that current databases do not fully represent the gut plasmidome. Interestingly, infants display greater plasmid diversity compared to mothers and other healthy adults. We find that Bacteroidota, a major bacterial phylum, serves as the primary host for gut plasmids and plays a dominant role in gut plasmid transfer events. Additionally, plasmids broaden the genetic capabilities of bacteria, with their influence on bacterial function becoming more apparent as children's gut microbiomes develop. This study sheds light on the role of plasmids in the infant gut microbiome, making a significant contribution to our understanding of plasmid biology.", "keywords": ["Adult", "Male", "0301 basic medicine", "0303 health sciences", "Bacteria", "Bacteroidetes", "Science", "Q", "Infant", " Newborn", "Infant", "Article", "Gastrointestinal Microbiome", "Feces", "03 medical and health sciences", "Humans", "Female", "Phylogeny", "Plasmids"]}, "links": [{"href": "https://doi.org/10.1038/s41467-024-51398-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-024-51398-3", "name": "item", "description": "10.1038/s41467-024-51398-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-024-51398-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-13T00:00:00Z"}}, {"id": "10.1093/femsre/fuaa015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:10Z", "type": "Journal Article", "created": "2020-05-20", "title": "The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health", "description": "ABSTRACT<p>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.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "human microbiome", "Review Article", "Gastrointestinal Microbiome", "3. Good health", "lactic acid bacteria", "03 medical and health sciences", "probiotics", "Health", "Lactobacillales", "food microbiome; human microbiome; lactic acid bacteria; probiotics", "food microbiome", "Food Microbiology", "Humans"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/811718/2/FEMSMicroRev%2c2020_LABfoodgut.pdf"}, {"href": "http://academic.oup.com/femsre/article-pdf/44/4/454/37084083/fuaa015.pdf"}, {"href": "https://doi.org/10.1093/femsre/fuaa015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Reviews", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsre/fuaa015", "name": "item", "description": "10.1093/femsre/fuaa015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsre/fuaa015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-18T00:00:00Z"}}, {"id": "10.1186/s12916-021-01913-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:10Z", "type": "Journal Article", "created": "2021-02-11", "title": "High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome", "description": "Abstract                 Background                 <p>Chronic inflammation, which can be modulated by diet, is linked to high white blood cell counts and correlates with higher cardiometabolic risk and risk of more severe infections, as in the case of COVID-19.</p>                                Methods                 <p>Here, we assessed the association between white blood cell profile (lymphocytes, basophils, eosinophils, neutrophils, monocytes and total white blood cells) as markers of chronic inflammation, habitual diet and gut microbiome composition (determined by sequencing of the 16S RNA) in 986 healthy individuals from the PREDICT-1 nutritional intervention study. We then investigated whether the gut microbiome mediates part of the benefits of vegetable intake on lymphocyte counts.</p>                                Results                 <p>Higher levels of white blood cells, lymphocytes and basophils were all significantly correlated with lower habitual intake of vegetables, with vegetable intake explaining between 3.59 and 6.58% of variation in white blood cells after adjusting for covariates and multiple testing using false discovery rate (q\uffe2\uff80\uff89&lt;\uffe2\uff80\uff890.1). No such association was seen with fruit intake. A mediation analysis found that 20.00% of the effect of vegetable intake on lymphocyte counts was mediated by one bacterial genus, Collinsella, known to increase with the intake of processed foods and previously associated with fatty liver disease. We further correlated white blood cells to other inflammatory markers including IL6 and GlycA, fasting and post-prandial glucose levels and found a significant relationship between inflammation and diet.</p>                                Conclusion                 <p>A habitual diet high in vegetables, but not fruits, is linked to a lower inflammatory profile for white blood cells, and a fifth of the effect is mediated by the genus Collinsella.</p>                                Trial registration                 <p>The ClinicalTrials.gov registration identifier is NCT03479866.</p>", "keywords": ["Adult", "Male", "0301 basic medicine", "610", "Leukocyte Count", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Leukocytes", "Humans", "Lymphocyte Count", "White blood cell", " Gut microbiome", " Diet", " Vegetable intake", " Chronic inflammation", "White blood cell", "Clostridium", "2. Zero hunger", "Gut microbiome", "Clostridiales", "0303 health sciences", "Mediation Analysis", "Interleukin-6", "R", "COVID-19", "Chronic inflammation; Diet; Gut microbiome; Vegetable intake; White blood cell", "Chronic inflammation", "General Medicine", "Fasting", "Middle Aged", "Diet", "Gastrointestinal Microbiome", "3. Good health", "Actinobacteria", "Vegetable intake", "Fruit", "Medicine", "Female", "Biomarkers", "Research Article"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1101012/2/s12916-021-01913-w.pdf"}, {"href": "https://iris.unitn.it/bitstream/11572/329112/1/s12916-021-01913-w.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1186/s12916-021-01913-w.pdf"}, {"href": "https://doi.org/10.1186/s12916-021-01913-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Medicine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12916-021-01913-w", "name": "item", "description": "10.1186/s12916-021-01913-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12916-021-01913-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-11T00:00:00Z"}}, {"id": "10.1101/2024.01.17.575993", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:18Z", "type": "Journal Article", "created": "2024-01-19", "title": "Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation", "description": "Abstract<p>Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challengingin vitroresulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.</p", "keywords": ["Anthelmintics", "Ivermectin", "Phenotype", "Bacteria", "QH301-705.5", "Ivermectin/pharmacology; Macrolides/pharmacology; Anthelmintics/pharmacology; Anti-Bacterial Agents/pharmacology; Bacteria/drug effects; Bacteria/growth & development; Gastrointestinal Microbiome/drug effects; Phenotype; Microbial Sensitivity Tests; Animals", "Animals", "Macrolides", "Microbial Sensitivity Tests", "Biology (General)", "Article", "Anti-Bacterial Agents", "Gastrointestinal Microbiome"]}, "links": [{"href": "https://doi.org/10.1101/2024.01.17.575993"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Communications%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2024.01.17.575993", "name": "item", "description": "10.1101/2024.01.17.575993", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2024.01.17.575993"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-18T00:00:00Z"}}, {"id": "11343/246714", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:24:35Z", "type": "Journal Article", "created": "2019-01-14", "title": "Exclusive dependence of IL-10R\u03b1 signalling on intestinal microbiota homeostasis and control of whipworm infection", "description": "The whipworm Trichuris trichiura is a soil-transmitted helminth that dwells in the epithelium of the caecum and proximal colon of their hosts causing the human disease, trichuriasis. Trichuriasis is characterized by colitis attributed to the inflammatory response elicited by the parasite while tunnelling through intestinal epithelial cells (IECs). The IL-10 family of receptors, comprising combinations of subunits IL-10R\u03b1, IL-10R\u03b2, IL-22R\u03b1 and IL-28R\u03b1, modulates intestinal inflammatory responses. Here we carefully dissected the role of these subunits in the resistance of mice to infection with T. muris, a mouse model of the human whipworm T. trichiura. Our findings demonstrate that whilst IL-22R\u03b1 and IL-28R\u03b1 are dispensable in the host response to whipworms, IL-10 signalling through IL-10R\u03b1 and IL-10R\u03b2 is essential to control caecal pathology, worm expulsion and survival during T. muris infections. We show that deficiency of IL-10, IL-10R\u03b1 and IL-10R\u03b2 results in dysbiosis of the caecal microbiota characterised by expanded populations of opportunistic bacteria of the families Enterococcaceae and Enterobacteriaceae. Moreover, breakdown of the epithelial barrier after whipworm infection in IL-10, IL-10R\u03b1 and IL-10R\u03b2-deficient mice, allows the translocation of these opportunistic pathogens or their excretory products to the liver causing organ failure and lethal disease. Importantly, bone marrow chimera experiments indicate that signalling through IL-10R\u03b1 and IL-10R\u03b2 in haematopoietic cells, but not IECs, is crucial to control worm expulsion and immunopathology. These findings are supported by worm expulsion upon infection of conditional mutant mice for the IL-10R\u03b1 on IECs. Our findings emphasize the pivotal and complex role of systemic IL-10R\u03b1 signalling on immune cells in promoting microbiota homeostasis and maintaining the intestinal epithelial barrier, thus preventing immunopathology during whipworm infections.", "keywords": ["0301 basic medicine", "Lydia Becker Institute", "QH301-705.5", "610", "Interleukin-22", "Mice", "03 medical and health sciences", "Animals", "Homeostasis", "Receptors", " Interleukin-10", "Trichuriasis", "Biology (General)", "Interleukins", "RC581-607", "Gastrointestinal Microbiome", "Interleukin-10", "3. Good health", "Intestines", "Mice", " Inbred C57BL", "Disease Models", " Animal", "Trichuris", "Cytokines", "Immunologic diseases. Allergy", "ResearchInstitutes_Networks_Beacons/lydia_becker_institute_of_immunology_and_inflammation; name=Lydia Becker Institute", "Research Article", "Signal Transduction"]}, "links": [{"href": "https://doi.org/11343/246714"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20Pathogens", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11343/246714", "name": "item", "description": "11343/246714", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11343/246714"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-14T00:00:00Z"}}, {"id": "1959.7/uws:64039", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:24:53Z", "type": "Journal Article", "created": "2019-04-15", "title": "Effects of diet on gut microbiota of soil collembolans", "description": "The importance of diet in regulating the gut microbiome of globally distributed and functionally important soil generalist invertebrates such as collembolans remain poorly understood. Here, we studied a model collembolan (Folsomia candida) and found that diet (bacteria, plant litters, yeast, mixed food) is a critical factor in regulating the microbial diversity and community composition of this important soil organism. Collembolans fed with litter exhibited the lowest bacterial diversity and were dominated by Ochrobactrum. Conversely, collembolans fed with mixed diets resulted in the highest bacterial diversity. Our findings further suggest that microbial communities associated with different diets are linked to different levels of collembolan fitness. For example, the relative abundance of the genera of unclassified Thermogemmatisporaceae, Brevibacillus, and Novosphingobium were positively correlated with growth of the collembolans. Together, our work provides evidence that diet is a major force controlling the gut microbiome of collembolans, and is a good environmental predictor for collembolan growth, with implications for ecosystem functioning in terrestrial environments.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Soil invertebrates", "0303 health sciences", "Microbiota", "Diets", "15. Life on land", "Diet", "Gastrointestinal Microbiome", "Soil", "03 medical and health sciences", "13. Climate action", "XXXXXX - Unknown", "Collembolans", "Animals", "Bacterial community", "Arthropods"]}, "links": [{"href": "https://doi.org/1959.7/uws:64039"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1959.7/uws:64039", "name": "item", "description": "1959.7/uws:64039", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:64039"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-01T00:00:00Z"}}, {"id": "38575018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:26:01Z", "type": "Journal Article", "created": "2024-04-02", "title": "Exploring the potential of earthworm gut bacteria for plastic degradation", "description": "The use of plastic mulch films in agriculture leads to the inevitable accumulation of plastic debris in soils. Here, we explored the potential of earthworm gut-inhabiting bacterial strains (Mycobacterium vanbaalenii (MV), Rhodococcus jostii (RJ), Streptomyces fulvissimus (SF), Bacillus simplex (BS), and Sporosarcina globispora (SG) to degrade plastic films (\u2300\u00a0=\u00a015\u00a0mm) made from commonly used polymers: low-density polyethylene film (LDPE-f), polylactic acid (PLA-f), polybutylene adipate terephthalate film (PBAT-f), and a commercial biodegradable mulch film, Bionov-B\u00ae (composed of Mater-Bi, a feedstock with PBAT, PLA and other chemical compounds). A 180-day experiment was conducted at room temperature (x\u0304 =19.4\u00a0\u00b0C) for different strain-plastic combinations under a low carbon media (0.1\u00d7 tryptic soy broth). Results showed that the tested strain-plastic combinations did not facilitate the degradation of LDPE-f (treated with RJ and SF), PBAT-f (treated with BS and SG), and Bionov-B (treated with BS, MV, and SG). However, incubating PLA-f with SF triggered a reduction in the molecular weights and an increase in crystallinity. Therefore, we used PLA-f as model plastic to study the influence of temperature ('room temperature' & '30\u00a0\u00b0C'), carbon source ('carbon-free' & 'low carbon supply'), and strain interactions ('single strains' & 'strain mixtures') on PLA degradation. SF and SF\u00a0+\u00a0RJ treatments significantly fostered PLA degradation under 30\u00a0\u00b0C in a low-carbon media. PLA-f did not show any degradation in carbon-free media treatments. The competition between different strains in the same system likely hindered the performance of PLA-degrading strains. A positive correlation between the final pH of culture media and PLA-f weight loss was observed, which might reflect the pH-dependent hydrolysis mechanism of PLA. Our results situate SF and its co-culture with RJ strains as possible accelerators of PLA degradation in temperatures below PLA glass transition temperature (Tg). Further studies are needed to test the bioremediation feasibility in soils.", "keywords": ["0301 basic medicine", "Bacteria", "ddc:550", "Polyesters", "01 natural sciences", "6. Clean water", "Gastrointestinal Microbiome", "03 medical and health sciences", "Biodegradation", " Environmental", "Life Science", "Animals", "Soil Pollutants", "Oligochaeta", "Plastics", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/38575018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "38575018", "name": "item", "description": "38575018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/38575018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-06-01T00:00:00Z"}}, {"id": "PMC11322291", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:27:39Z", "type": "Journal Article", "created": "2024-08-13", "title": "Insights into the ecology of the infant gut plasmidome", "description": "Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate the gut microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow to understand the impact of plasmids on the gut microbiome. We create a plasmid phylogenetic tree, devise a method for assigning plasmid hosts, and examine potential plasmid transfer networks. Our research discovers a wide variety of previously unidentified plasmid sequences, indicating that current databases do not fully represent the gut plasmidome. Interestingly, infants display greater plasmid diversity compared to mothers and other healthy adults. We find that Bacteroidota, a major bacterial phylum, serves as the primary host for gut plasmids and plays a dominant role in gut plasmid transfer events. Additionally, plasmids broaden the genetic capabilities of bacteria, with their influence on bacterial function becoming more apparent as children's gut microbiomes develop. This study sheds light on the role of plasmids in the infant gut microbiome, making a significant contribution to our understanding of plasmid biology.", "keywords": ["Adult", "Male", "0301 basic medicine", "0303 health sciences", "Bacteria", "Bacteroidetes", "Science", "Q", "Infant", " Newborn", "Infant", "Article", "Gastrointestinal Microbiome", "Feces", "03 medical and health sciences", "Humans", "Female", "Phylogeny", "Plasmids"]}, "links": [{"href": "https://doi.org/PMC11322291"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11322291", "name": "item", "description": "PMC11322291", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11322291"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-13T00:00:00Z"}}, {"id": "PMC11603213", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:27:40Z", "type": "Journal Article", "created": "2024-01-19", "title": "Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation", "description": "Abstract<p>Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challengingin vitroresulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.</p", "keywords": ["Anthelmintics", "Ivermectin", "Phenotype", "Bacteria", "QH301-705.5", "Ivermectin/pharmacology; Macrolides/pharmacology; Anthelmintics/pharmacology; Anti-Bacterial Agents/pharmacology; Bacteria/drug effects; Bacteria/growth & development; Gastrointestinal Microbiome/drug effects; Phenotype; Microbial Sensitivity Tests; Animals", "Animals", "Macrolides", "Microbial Sensitivity Tests", "Biology (General)", "Article", "Anti-Bacterial Agents", "Gastrointestinal Microbiome"]}, "links": [{"href": "https://doi.org/PMC11603213"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Communications%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11603213", "name": "item", "description": "PMC11603213", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11603213"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-18T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Gastrointestinal+Microbiome&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Gastrointestinal+Microbiome&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Gastrointestinal+Microbiome&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Gastrointestinal+Microbiome&offset=14", "hreflang": "en-US"}], "numberMatched": 14, "numberReturned": 14, "distributedFeatures": [], "timeStamp": "2026-05-25T00:06:38.273579Z"}