Development of Bifidobacterium spp. in infants: Age dependent patterns and correlating factors

Mastergradsoppgave i næringsrettet bioteknologi, Avdeling for lærerutdanning og naturvitenskap, Høgskolen i Hedmark, 2011. Master of applied and commercial biotechnology.Bifidobacteria are a major microbial component of infant gut microbiota which is believed to promote health benefits for the host and stimulate the maturation of immune system. Despite the importance we know little about the natural development of bifidobacteria in the infant gut. To address this question, we analyzed mixed Bifidobacterium clpC gene sequences from IMPACT (Immunology and Microbiology in Prevention of Allergy among Children in Trondheim) stool samples of 83 infants and their mothers using the novel multivariate statistical MCR-ALS approach. We also developed a novel basecaller script in MATLAB® environment which simplifies the use of the MCR-ALS method so that manual decoding is no longer required. Faecal material was sampled during the first and the second part of pregnancy, at 3 days, 10 days, 4 months, 1 year and 2 years after birth. Five dominant Bifidobacterium species were identified and verified by cloning. Stool samples were predicted to be rich in B. adolescentis, B. bifidum, B. dentium, B. breve and B. longum species. The B. longum group consisted of B. longum longum irrespective of age, however B. longum infantis was mostly identified in four-month-old individuals indicating a potential infant-to-infant nature of its transmittance. Local Similarity Analysis revealed self-supportive correlations between Bifidobacterium, Lactobacillales, Clostridium, Proteobacteria and other bacterial groups. The amount of B. breve in infants correlated with the incidence of common cold infections during pregnancy. Development of all Bifidobacterium and B. longum groups had correlation to the occurrence of vaginal fungal infection during pregnancy. Elevated amounts of B. adolescentis in four-month-old infants correlated to high IgE levels and eczema symptoms, while levels of the B. longum group in infants – to eczema. In conclusion, new patterns in bifidobacterial development and interaction are described. We believe this new knowledge will be important for the future understanding of bifidobacteria in health and disease

Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates

Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.publishedVersio

Fighting Antibiotic Resistance in Hospital-Acquired Infections: Current State and Emerging Technologies in Disease Prevention, Diagnostics and Therapy

Rising antibiotic resistance is a global threat that is projected to cause more deaths than all cancers combined by 2050. In this review, we set to summarize the current state of antibiotic resistance, and to give an overview of the emerging technologies aimed to escape the pre-antibiotic era recurrence. We conducted a comprehensive literature survey of >150 original research and review articles indexed in the Web of Science using “antimicrobial resistance,” “diagnostics,” “therapeutics,” “disinfection,” “nosocomial infections,” “ESKAPE pathogens” as key words. We discuss the impact of nosocomial infections on the spread of multi-drug resistant bacteria, give an overview over existing and developing strategies for faster diagnostics of infectious diseases, review current and novel approaches in therapy of infectious diseases, and finally discuss strategies for hospital disinfection to prevent MDR bacteria spread.publishedVersio

Diet-dependent modular dynamic interactions of the equine cecal microbiota

Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg(−1) body weight per day) and a fiber-rich diet of only hay. Cecal contents were sampled via the cannula each h for 24 h for both diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich diet, with Streptococcus spp. and Anaerovibrio spp. showing the largest fluctuations. Shotgun metagenome sequencing revealed that diet differences may be explained by modular switches in metabolic cross-feeding between microbial consortia in which fermentation is linked to sugar alcohols and amino sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding

Etablering av tarmflora i spedbarn fra en stor norsk kohort

Human gut microbiota, our so-called forgotten organ, is crucial for proper functioning of our body and for health maintenance. Although the topic of the gut microbiota establishment is very important, scientists still have limited knowledge on the subject. The reason for this knowledge gap partly stems from the lack of large longitudinal studies. The aim of this thesis was therefore to assess the development of gut microbial community in infants using information from a large cohort. We collectively analyzed 16S rRNA gene amplicons from stool samples of about 350 mother and child pairs followed from pregnancy up to two years of age using various sequencing techniques.Menneskets tarm flora, såkalt ‘det glemte organet vårt’, er avgjørende for en korrekt funksjon av vår kropp og vedlikehold av vår helse. Selv om temaet om etablering av tarmen bakterieflora er svært viktig, har forskere fortsatt en svært begrenset kunnskap om emnet. Grunnen til den begrensingen stammer delvis fra mangel på store studiekohorter over tid. Målet med denne oppgaven var derfor å vurdere utviklingen av tarmflora hos spedbarn ved bruk av en stor kohort. Vi kollektivt analyserte den mikrobielle sammensetning i avføringsprøver fra ca. 350 mor og barn par som var fulgt fra svangerskapet opp til to år

Development of Bifidobacterium spp. in infants: Age dependent patterns and correlating factors

Mastergradsoppgave i næringsrettet bioteknologi, Avdeling for lærerutdanning og naturvitenskap, Høgskolen i Hedmark, 2011. Master of applied and commercial biotechnology.Bifidobacteria are a major microbial component of infant gut microbiota which is believed to promote health benefits for the host and stimulate the maturation of immune system. Despite the importance we know little about the natural development of bifidobacteria in the infant gut. To address this question, we analyzed mixed Bifidobacterium clpC gene sequences from IMPACT (Immunology and Microbiology in Prevention of Allergy among Children in Trondheim) stool samples of 83 infants and their mothers using the novel multivariate statistical MCR-ALS approach. We also developed a novel basecaller script in MATLAB® environment which simplifies the use of the MCR-ALS method so that manual decoding is no longer required. Faecal material was sampled during the first and the second part of pregnancy, at 3 days, 10 days, 4 months, 1 year and 2 years after birth. Five dominant Bifidobacterium species were identified and verified by cloning. Stool samples were predicted to be rich in B. adolescentis, B. bifidum, B. dentium, B. breve and B. longum species. The B. longum group consisted of B. longum longum irrespective of age, however B. longum infantis was mostly identified in four-month-old individuals indicating a potential infant-to-infant nature of its transmittance. Local Similarity Analysis revealed self-supportive correlations between Bifidobacterium, Lactobacillales, Clostridium, Proteobacteria and other bacterial groups. The amount of B. breve in infants correlated with the incidence of common cold infections during pregnancy. Development of all Bifidobacterium and B. longum groups had correlation to the occurrence of vaginal fungal infection during pregnancy. Elevated amounts of B. adolescentis in four-month-old infants correlated to high IgE levels and eczema symptoms, while levels of the B. longum group in infants – to eczema. In conclusion, new patterns in bifidobacterial development and interaction are described. We believe this new knowledge will be important for the future understanding of bifidobacteria in health and disease

Establishment of gut microbiota in infants from a large Norwegian cohort

Human gut microbiota, our so-called forgotten organ, is crucial for proper functioning of our body and for health maintenance. Although the topic of the gut microbiota establishment is very important, scientists still have limited knowledge on the subject. The reason for this knowledge gap partly stems from the lack of large longitudinal studies. The aim of this thesis was therefore to assess the development of gut microbial community in infants using information from a large cohort. We collectively analyzed 16S rRNA gene amplicons from stool samples of about 350 mother and child pairs followed from pregnancy up to two years of age using various sequencing techniques

Gut microbiota in HIV infection: Implication for disease progression and management

Survival rates among HIV patients have significantly improved since the introduction of antiretroviral therapy (ART) in HIV management. However, persistent disease progression and clinical complications in virally suppressed individuals point to additional contributing factors other than HIV replication; microbial translocation is one such factor. The role of underlying commensal microbes and microbial products that traverse the intestinal lumen into systemic circulation in the absence of overt bacteraemia is under current investigation. This review focuses on current knowledge of the complex microbial communities and microbial markers involved in the disruption of mucosal immune T-cells in the promotion of inflammatory processes in HIV infections. Unanswered questions and aims for future studies are addressed. We provide perspective for discussing potential future therapeutic strategies focused on modulating the gut microbiota to abate HIV disease progression

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results