{"entity": "journal", "iuid": "f23a7234a4a944879d6f6de9c7498e58", "timestamp": "2026-06-07T20:03:01.380Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/mSystems.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/mSystems"}}, "title": "mSystems", "issn": "2379-5077", "issn-l": "2379-5077", "publications_count": 10, "publications": [{"entity": "publication", "iuid": "7472b08ff92e401f907b54144ee97ed0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7472b08ff92e401f907b54144ee97ed0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7472b08ff92e401f907b54144ee97ed0"}}, "title": "Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings.", "authors": [{"family": "Calderon Toledo", "given": "Carla", "initials": "C", "orcid": "0000-0001-9483-9891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8c67b3b7435453396d0fd62636838e3.json"}}, {"family": "von Mentzer", "given": "Astrid", "initials": "A", "orcid": "0000-0002-2167-1394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36cefe255ba14d8684826fae58598036.json"}}, {"family": "Agramont", "given": "Jorge", "initials": "J"}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Zhou", "given": "Yingshun", "initials": "Y"}, {"family": "Szab\u00f3", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Colque", "given": "Patricia", "initials": "P"}, {"family": "Kuhn", "given": "Inger", "initials": "I"}, {"family": "Guti\u00e9rrez-Cortez", "given": "Sergio", "initials": "S", "orcid": "0000-0001-6181-6554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ef7d00721e143df9ae40299cb131fff.json"}}, {"family": "Joffr\u00e9", "given": "Enrique", "initials": "E", "orcid": "0000-0003-0328-518X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0a7d88da85f4dbfab455ac2df10a8de.json"}}], "type": "journal article", "published": "2023-10-26", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "8", "issue": "5", "pages": "e0014123", "issn-l": "2379-5077"}, "abstract": "The importance of clean water cannot be overstated. It is a vital resource for maintaining health and well-being. Unfortunately, water sources contaminated with fecal discharges from animal and human origin due to a lack of wastewater management pose a significant risk to communities, as they can become a means of transmission of pathogenic bacteria like enterotoxigenic E. coli (ETEC). ETEC is frequently found in polluted water in countries with a high prevalence of diarrheal diseases, such as Bolivia. This study provides novel insights into the circulation of ETEC between diarrheal cases and polluted water sources in areas with high rates of diarrheal disease. These findings highlight the Choqueyapu River as a potential reservoir for emerging pathogens carrying antibiotic-resistance genes, making it a crucial area for monitoring and intervention. Furthermore, the results demonstrate the feasibility of a low-cost, high-throughput method for tracking bacterial pathogens in low- and middle-income countries, making it a valuable tool for One Health monitoring efforts.", "doi": "10.1128/msystems.00141-23", "pmid": "37681982", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10654058"}], "notes": [], "created": "2025-12-02T15:47:10.590Z", "modified": "2025-12-02T15:47:10.700Z"}, {"entity": "publication", "iuid": "3850e611ca8445ce85ce463d00f4398e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3850e611ca8445ce85ce463d00f4398e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3850e611ca8445ce85ce463d00f4398e"}}, "title": "Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort.", "authors": [{"family": "Y\u0131ld\u0131r\u0131m", "given": "S\u00fcleyman", "initials": "S", "orcid": "0000-0002-2752-1223", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9af0d67611a84605a753955dc52eaaa0.json"}}, {"family": "Nalbanto\u011flu", "given": "\u00d6zkan Ufuk", "initials": "\u00d6U"}, {"family": "Bayraktar", "given": "Abdulahad", "initials": "A"}, {"family": "Ercan", "given": "Fatma Bet\u00fcl", "initials": "FB"}, {"family": "G\u00fcndo\u011fdu", "given": "Aycan", "initials": "A"}, {"family": "Velio\u011flu", "given": "Halil Aziz", "initials": "HA"}, {"family": "G\u00f6l", "given": "Mehmet Fatih", "initials": "MF"}, {"family": "Soylu", "given": "Ayten Ekinci", "initials": "AE"}, {"family": "Ko\u00e7", "given": "Fatma", "initials": "F"}, {"family": "G\u00fclp\u0131nar", "given": "Ezgi Aslan", "initials": "EA"}, {"family": "Kadak", "given": "K\u00fcbra Sogukkanl\u0131", "initials": "KS"}, {"family": "Ar\u0131kan", "given": "Muzaffer", "initials": "M"}, {"family": "Mardino\u011flu", "given": "Adil", "initials": "A"}, {"family": "Ko\u00e7ak", "given": "Mehmet", "initials": "M"}, {"family": "K\u00f6seo\u011flu", "given": "Emel", "initials": "E"}, {"family": "Hano\u011flu", "given": "L\u00fctf\u00fc", "initials": "L"}], "type": "journal article", "published": "2022-02-22", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "7", "issue": "1", "pages": "e0000422", "issn-l": "2379-5077"}, "abstract": "Alzheimer's disease (AD) is a heterogeneous disorder that spans a continuum with multiple phases, including preclinical, mild cognitive impairment, and dementia. Unlike for most other chronic diseases, human studies reporting on AD gut microbiota in the literature are very limited. With the scarcity of approved drugs for AD therapies, the rational and precise modulation of gut microbiota composition using diet and other tools is a promising approach to the management of AD. Such an approach could be personalized if an AD continuum can first be deconstructed into multiple strata based on specific microbiota features by using single or multiomics techniques. However, stratification of AD gut microbiota has not been systematically investigated before, leaving an important research gap for gut microbiota-based therapeutic approaches. Here, we analyze 16S rRNA amplicon sequencing of stool samples from 27 patients with mild cognitive impairment, 47 patients with AD, and 51 nondemented control subjects by using tools compatible with the compositional nature of microbiota. To stratify the AD gut microbiota community, we applied four machine learning techniques, including partitioning around the medoid clustering and fitting a probabilistic Dirichlet mixture model, the latent Dirichlet allocation model, and we performed topological data analysis for population-scale microbiome stratification based on the Mapper algorithm. These four distinct techniques all converge on Prevotella and Bacteroides stratification of the gut microbiota across the AD continuum, while some methods provided fine-scale resolution in stratifying the community landscape. Finally, we demonstrate that the signature taxa and neuropsychometric parameters together robustly classify the groups. Our results provide a framework for precision nutrition approaches aiming to modulate the AD gut microbiota. IMPORTANCE The prevalence of AD worldwide is estimated to reach 131 million by 2050. Most disease-modifying treatments and drug trials have failed, due partly to the heterogeneous and complex nature of the disease. Recent studies demonstrated that gut dybiosis can influence normal brain function through the so-called \"gut-brain axis.\" Modulation of the gut microbiota, therefore, has drawn strong interest in the clinic in the management of the disease. However, there is unmet need for microbiota-informed stratification of AD clinical cohorts for intervention studies aiming to modulate the gut microbiota. Our study fills in this gap and draws attention to the need for microbiota stratification as the first step for microbiota-based therapy. We demonstrate that while Prevotella and Bacteroides clusters are the consensus partitions, the newly developed probabilistic methods can provide fine-scale resolution in partitioning the AD gut microbiome landscape.", "doi": "10.1128/msystems.00004-22", "pmid": "35133187", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8823292"}], "notes": [], "created": "2023-12-04T15:04:47.514Z", "modified": "2023-12-04T15:04:47.557Z"}, {"entity": "publication", "iuid": "1d401637ed07449389902814b1acbdd2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d401637ed07449389902814b1acbdd2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d401637ed07449389902814b1acbdd2"}}, "title": "Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df5f980a4dfb4b669961af28a1242f12.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tsuji", "given": "Jackson M", "initials": "JM"}, {"family": "Neufeld", "given": "Josh D", "initials": "JD", "orcid": "0000-0002-8722-8571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43f0e496fcd548dca2475d478a6d0907.json"}}, {"family": "McMahon", "given": "Katherine D", "initials": "KD", "orcid": "0000-0002-7038-026X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65e07397a409477795c29260f2260709.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Greening", "given": "Chris", "initials": "C", "orcid": "0000-0001-7616-0594", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1637996ba33748608349dbee48e8fdb9.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9a0edb050549978d1f489fb98017b3.json"}}], "type": "journal article", "published": "2021-05-11", "journal": {"title": "mSystems", "issn": "2379-5077", "issn-l": "2379-5077", "volume": "6", "issue": "3", "pages": null}, "abstract": "Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or \"species\"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to \u223c60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.", "doi": "10.1128/mSystems.01196-20", "pmid": "33975970", "labels": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "6/3/e01196-20"}, {"db": "pmc", "key": "PMC8125076"}], "notes": [], "created": "2021-05-17T13:48:19.992Z", "modified": "2022-11-04T11:32:13.276Z"}, {"entity": "publication", "iuid": "06d7fb39d5064a0e8feba280f484b698", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/06d7fb39d5064a0e8feba280f484b698.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/06d7fb39d5064a0e8feba280f484b698"}}, "title": "Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts.", "authors": [{"family": "Mondav", "given": "Rhiannon", "initials": "R", "orcid": "0000-0002-5574-5531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62798f5de4194f4eb1a56da3d5f57ce2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fd9423637a54230892379a5b50cf47f.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Langenheder", "given": "Silke", "initials": "S", "orcid": "0000-0002-5245-9935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59f0127345a144f19341dec60090b588.json"}}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3afeabbf8464b2480b4daee3774a0b7.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df5f980a4dfb4b669961af28a1242f12.json"}}], "type": "journal article", "published": "2020-09-29", "journal": {"title": "mSystems", "issn": "2379-5077", "issn-l": "2379-5077", "volume": "5", "issue": "5", "pages": null}, "abstract": "While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera \"Candidatus Planktophila\" (acI-A) and \"Candidatus Nanopelagicus\" (acI-B) and the proteobacterial genus \"Candidatus Fonsibacter\" (LD12). While \"Ca Planktophila\" and \"Ca. Fonsibacter\" had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which \"Ca Planktophila\" is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain \"Ca Planktophila\" population abundance, the success of \"Ca. Nanopelagicus\" and \"Ca. Fonsibacter\" is better explained as a community by-product. Ecotype differentiation of \"Ca. Fonsibacter\" as a means of escaping predation was supported but not for overcoming auxotrophies.IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: \"Ca Planktophila\" (acI-A), \"Ca. Nanopelagicus\" (acI-B), and \"Ca. Fonsibacter\" (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.", "doi": "10.1128/mSystems.00316-20", "pmid": "32994284", "labels": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "5/5/e00316-20"}, {"db": "pmc", "key": "PMC7527133"}], "notes": [], "created": "2020-11-05T17:28:43.744Z", "modified": "2022-11-04T11:32:14.371Z"}, {"entity": "publication", "iuid": "78af8adee55f47dfa9e09da18f49e2ca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/78af8adee55f47dfa9e09da18f49e2ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/78af8adee55f47dfa9e09da18f49e2ca"}}, "title": "Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation", "authors": [{"family": "Karlsen", "given": "Jan", "initials": "J", "orcid": "0000-0002-2821-9026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a1c2fa8404749b0a797e90e9c6cb09e.json"}}, {"family": "Asplund-Samuelsson", "given": "Johannes", "initials": "J", "orcid": "0000-0001-8077-5305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1cf0c49cbb849b194b0b46582441d09.json"}}, {"family": "Thomas", "given": "Quentin", "initials": "Q", "orcid": "0000-0002-3522-5125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6fa033a00e46d0b068dcdebd13a25e.json"}}, {"family": "Jahn", "given": "Michael", "initials": "M", "orcid": "0000-0002-3913-153X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce2ef4c47b24946876c12a549785e36.json"}}, {"family": "Hudson", "given": "Elton P", "initials": "EP", "orcid": "0000-0003-1899-7649", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b1c894d4c8b48569b9879d0342b91dd.json"}}], "type": "journal-article", "published": "2018-10-30", "journal": {"title": "mSystems", "issn": "2379-5077", "issn-l": "2379-5077", "volume": "3", "issue": "5", "pages": null}, "abstract": null, "doi": "10.1128/msystems.00126-18", "pmid": null, "labels": {"Paul Hudson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-10-09T09:04:52.450Z", "modified": "2022-11-04T11:32:17.185Z"}, {"entity": "publication", "iuid": "fe0df6a374124b54b9dba430f3fe7edd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe0df6a374124b54b9dba430f3fe7edd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe0df6a374124b54b9dba430f3fe7edd"}}, "title": "Bacteriophages Synergize with the Gut Microbial Community To Combat Salmonella.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Bengtsson", "given": "Carina", "initials": "C"}, {"family": "Alisjahbana", "given": "Arlisa", "initials": "A"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Kamal", "given": "Anaga", "initials": "A"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Midtvedt", "given": "Tore", "initials": "T"}, {"family": "Norin", "given": "Elisabeth", "initials": "E"}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2018-10-02", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "3", "issue": "5", "issn-l": "2379-5077"}, "abstract": "Salmonella infection is one of the main causes of food-borne diarrheal diseases worldwide. Although most Salmonella infections can be cleared without treatment, some cause serious illnesses that require antibiotic treatment. In view of the growing emergence of antibiotic-resistant Salmonella strains, novel treatments are increasingly required. Furthermore, there is a striking paucity of data on how a balanced human gut microbiota responds to Salmonella infection. This study aimed to evaluate whether a balanced gut microbiota protects against Salmonella growth and to compare two antimicrobial approaches for managing Salmonella infection: bacteriophage (phage) treatment and antibiotic treatment. Anaerobically cultivated human intestinal microflora (ACHIM) is a feasible model for the human gut microbiota and naturally inhibits Salmonella infection. By mimicking Salmonella infection in vitro using ACHIM, we observed a large reduction of Salmonella growth by the ACHIM itself. Treatments with phage and antibiotic further inhibited Salmonella growth. However, phage treatment had less impact on the nontargeted bacteria in ACHIM than the antibiotic treatment did. Phage treatment has high specificity when combating Salmonella infection and offers a noninvasive alternative to antibiotic treatment. IMPORTANCE Antibiotic-resistant bacteria are a global threat. Therefore, alternative approaches for combatting bacteria, especially antibiotic-resistant bacteria, are urgently needed. Using a human gut microbiota model, we demonstrate that bacteriophages (phages) are able to substantially decrease pathogenic Salmonella without perturbing the microbiota. Conversely, antibiotic treatment leads to the eradication of close to all commensal bacteria, leaving only antibiotic-resistant bacteria. An unbalanced microbiota has been linked to many diseases both in the gastrointestinal tract or \"nonintestinal\" diseases. In our study, we show that the microbiota provides a protective effect against Salmonella. Since phage treatment preserves the healthy gut microbiota, it is a feasible superior alternative to antibiotic treatment. Furthermore, when combating infections caused by pathogenic bacteria, gut microbiota should be considered.", "doi": "10.1128/mSystems.00119-18", "pmid": "30320220", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6172775"}, {"db": "pii", "key": "mSystems00119-18"}], "notes": [], "created": "2022-11-08T07:01:11.963Z", "modified": "2023-10-27T09:33:52.189Z"}, {"entity": "publication", "iuid": "c7a8997484b1449ea6908abb6134cf37", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c7a8997484b1449ea6908abb6134cf37.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c7a8997484b1449ea6908abb6134cf37"}}, "title": "Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions.", "authors": [{"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tan", "given": "BoonFei", "initials": "B"}, {"family": "Foght", "given": "Julia", "initials": "J"}, {"family": "Wendeberg", "given": "Annelie", "initials": "A"}, {"family": "Berry", "given": "David", "initials": "D"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2017-10-31", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "2", "issue": "5", "issn-l": "2379-5077"}, "abstract": "Syntrophy among ", "doi": "10.1128/mSystems.00038-17", "pmid": "29104938", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "mSystems00038-17"}, {"db": "pmc", "key": "PMC5663940"}], "notes": [], "created": "2018-12-05T12:26:24.735Z", "modified": "2018-12-05T12:26:24.752Z"}, {"entity": "publication", "iuid": "9f409012909d4ee9a7622603fced2b68", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9f409012909d4ee9a7622603fced2b68.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9f409012909d4ee9a7622603fced2b68"}}, "title": "Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.", "authors": [{"family": "Hamilton", "given": "Joshua J", "initials": "JJ"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Brown", "given": "Brittany S", "initials": "BS"}, {"family": "Oyserman", "given": "Ben O", "initials": "BO"}, {"family": "Moya-Flores", "given": "Francisco", "initials": "F"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Malmstrom", "given": "Rex R", "initials": "RR"}, {"family": "Forest", "given": "Katrina T", "initials": "KT"}, {"family": "McMahon", "given": "Katherine D", "initials": "KD"}], "type": "journal article", "published": "2017-08-29", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "2", "issue": "4", "issn-l": "2379-5077"}, "abstract": "An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the \"seed set framework,\" which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482-14487, 2008, https://doi.org/10.1073/pnas.0806162105), enables computational analysis of metabolic reconstructions while providing new insights into a microbe's metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs. IMPORTANCE The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism's metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes.", "doi": "10.1128/mSystems.00091-17", "pmid": "28861526", "labels": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "mSystems00091-17"}, {"db": "pmc", "key": "PMC5574706"}], "notes": [], "created": "2020-11-05T17:27:37.209Z", "modified": "2022-11-07T11:37:23.379Z"}, {"entity": "publication", "iuid": "3d1d3533ccab48c997c292971e59224a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d1d3533ccab48c997c292971e59224a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d1d3533ccab48c997c292971e59224a"}}, "title": "The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.", "authors": [{"family": "Zeigler Allen", "given": "Lisa", "initials": "L"}, {"family": "McCrow", "given": "John P", "initials": "JP"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Badger", "given": "Jonathan H", "initials": "JH"}, {"family": "Hoffman", "given": "Jeffery M", "initials": "JM"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Venter", "given": "J Craig", "initials": "JC"}], "type": "journal article", "published": "2017-02-14", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "2", "issue": "1", "issn-l": "2379-5077"}, "abstract": "Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetr\u00e4sk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order ", "doi": "10.1128/mSystems.00125-16", "pmid": "28217745", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "mSystems00125-16"}, {"db": "pmc", "key": "PMC5309335"}], "notes": [], "created": "2018-12-05T12:56:55.946Z", "modified": "2018-12-05T12:56:55.965Z"}, {"entity": "publication", "iuid": "cac6310a3ed24520931b4fcc8ad9e815", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cac6310a3ed24520931b4fcc8ad9e815.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cac6310a3ed24520931b4fcc8ad9e815"}}, "title": "Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus.", "authors": [{"family": "Casey", "given": "John R", "initials": "JR", "orcid": "0000-0002-8630-0551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc7abfbf1614dd78a61c32cd631d377.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Karl", "given": "David M", "initials": "DM"}], "type": "journal article", "published": "2016-11-15", "journal": {"title": "mSystems", "issn": "2379-5077", "issn-l": "2379-5077", "volume": "1", "issue": "6", "pages": null}, "abstract": "Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794 reactions involving 680 metabolites distributed in 6 subcellular locations. iJC568 was used to quantify metabolic fluxes under PLG conditions, and we observed a close correspondence between experimental and computed fluxes. We found that MED4 has minimized its dependence on intracellular phosphate, not only through drastic depletion of phosphorus-containing biomass components but also through network-wide reductions in phosphate-reaction participation and the loss of a key enzyme, succinate dehydrogenase. These alterations occur despite the stringency of having relatively few pathway redundancies and an extremely high proportion of essential metabolic genes (47%; defined as the percentage of lethal in silico gene knockouts). These strategies are examples of nutrient-controlled adaptive evolution and confer a dramatic growth rate advantage to MED4 in phosphorus-limited regions. IMPORTANCE Microbes are known to employ three basic strategies to compete for limiting elemental resources: (i) cell quotas may be adjusted by alterations to cell physiology or by substitution of a more plentiful resource, (ii) stressed cells may synthesize high-affinity transporters, and (iii) cells may access more costly sources from internal stores, by degradation, or by petitioning other microbes. In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan cyanobacterium Prochlorococcus marinus thrives by adopting all three strategies and a fourth, previously unknown strategy. By generating a detailed model of its metabolism, we found that strain MED4 has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, despite the stringency of nearly half of its metabolic genes being essential for survival. Relieving phosphorus limitation, both physiologically and throughout intermediate metabolism, substantially improves phosphorus-specific growth rates.", "doi": "10.1128/mSystems.00065-16", "pmid": "27868089", "labels": {"Affiliated researcher": null, "Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "mSystems00065-16"}, {"db": "pmc", "key": "PMC5111396"}], "notes": [], "created": "2018-12-03T14:41:30.127Z", "modified": "2022-11-04T11:32:19.218Z"}], "created": "2018-12-03T14:41:30.140Z", "modified": "2020-11-27T13:12:59.867Z"}