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Article ; Online: Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly

Tongyuan Hu / Jianwei Chen / Xiaoqian Lin / Wenxin He / Hewei Liang / Mengmeng Wang / Wenxi Li / Zhinan Wu / Mo Han / Xin Jin / Karsten Kristiansen / Liang Xiao / Yuanqiang Zou

Scientific Reports, Vol 14, Iss 1, Pp 1-

2024 Volume 9

Abstract: Abstract The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of ... ...

Abstract	Abstract The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
Keywords	Medicine ; R ; Science ; Q
Subject code	572 ; 612
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chord

Ke-Xu Xiong / Han-Lin Zhou / Cong Lin / Jian-Hua Yin / Karsten Kristiansen / Huan-Ming Yang / Gui-Bo Li

Communications Biology, Vol 5, Iss 1, Pp 1-

an ensemble machine learning algorithm to identify doublets in single-cell RNA sequencing data

2022 Volume 11

Abstract: For the unmet need to choose the suitable doublet detection method, an ensemble machine learning algorithm called Chord was developed, which integrates multiple methods and achieves higher accuracy and stability on different scRNA-seq datasets. ...

Abstract	For the unmet need to choose the suitable doublet detection method, an ensemble machine learning algorithm called Chord was developed, which integrates multiple methods and achieves higher accuracy and stability on different scRNA-seq datasets.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Gluten-Free Diet during Pregnancy and Early Life Increases Short Chain Fatty Acid-Producing Bacteria and Regulatory T Cells in Prediabetic NOD Mice

Valdemar Brimnes Ingemann Johansen / Daisy Færø / Karsten Buschard / Karsten Kristiansen / Flemming Pociot / Pia Kiilerich / Knud Josefsen / Martin Haupt-Jorgensen / Julie Christine Antvorskov

Cells, Vol 12, Iss 1567, p

2023 Volume 1567

Abstract: The incidence of the autoimmune disease type 1 diabetes is increasing, likely caused by environmental factors. A gluten-free diet has previously been shown to ameliorate autoimmune diabetes in non-obese diabetic (NOD) mice and humans. Although the exact ... ...

Abstract	The incidence of the autoimmune disease type 1 diabetes is increasing, likely caused by environmental factors. A gluten-free diet has previously been shown to ameliorate autoimmune diabetes in non-obese diabetic (NOD) mice and humans. Although the exact mechanisms are not understood, interventions influencing the intestinal microbiota early in life affect the risk of type 1 diabetes. Here, we characterize how NOD mice that are fed a gluten-free (GF) diet differ from NOD mice that are fed a gluten-containing standard (STD) diet in terms of their microbiota composition by 16S rRNA gene amplicon sequencing and pancreatic immune environment by real-time quantitative PCR at the prediabetic stage at 6 and 13 weeks of age. Gut microbiota analysis revealed highly distinct microbiota compositions in both the cecum and the colon of GF-fed mice compared with STD-fed mice. The microbiotas of the GF-fed mice were characterized by an increased Firmicutes / Bacteroidetes ratio, an increased abundance of short chain fatty acid (particularly butyrate)-producing bacteria, and a reduced abundance of Lactobacilli compared with STD mice. We found that the insulitis score in the GF mice was significantly reduced compared with the STD mice and that the markers for regulatory T cells and T helper 2 cells were upregulated in the pancreas of the GF mice. In conclusion, a GF diet during pre- and early post-natal life induces shifts in the cecal and colonic microbiota compatible with a less inflammatory environment, providing a likely mechanism for the protective effect of a GF diet in humans.
Keywords	type 1 diabetes ; gut microbiota ; regulatory T cells ; short chain fatty acids ; autoimmunity ; dietary factors ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats

Melissa R. Ingala / Daniel J. Becker / Jacob Bak Holm / Karsten Kristiansen / Nancy B. Simmons

Ecology and Evolution, Vol 9, Iss 11, Pp 6508-

2019 Volume 6523

Abstract: Abstract Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free‐ranging animals. Rapid land‐ ... ...

Abstract	Abstract Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free‐ranging animals. Rapid land‐use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land‐use change on wildlife microbiotas, we analyzed long‐term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross‐species pathogen transmission.
Keywords	Desmodus rotundus ; diet homogenization ; land‐use change ; livestock ; microbiota ; resource provisioning ; Ecology ; QH540-549.5
Subject code	333
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism

Xiangwei Hu / Kai Xia / Minhui Dai / Xiaofeng Han / Peng Yuan / Jia Liu / Shiwei Liu / Fuhuai Jia / Jiayu Chen / Fangfang Jiang / Jieyao Yu / Huanming Yang / Jian Wang / Xun Xu / Xin Jin / Karsten Kristiansen / Liang Xiao / Wei Chen / Mo Han /

Shenglin Duan

npj Biofilms and Microbiomes, Vol 9, Iss 1, Pp 1-

2023 Volume 9

Abstract: Abstract Intermittent fasting (IF) is a promising paradigm for weight loss which has been shown to modulate the gut microbiota based on 16S rRNA gene amplicon sequencing. Here, 72 Chinese volunteers with a wide range of body mass index (BMI) participated ...

Abstract	Abstract Intermittent fasting (IF) is a promising paradigm for weight loss which has been shown to modulate the gut microbiota based on 16S rRNA gene amplicon sequencing. Here, 72 Chinese volunteers with a wide range of body mass index (BMI) participated in a three-week IF program during which an average loss of 3.67 kg body weight accompanied with improved clinical parameters was observed irrespective of initial anthropometric and gut microbiota status. Fecal samples were collected before and after the intervention and subjected to shotgun metagenomic sequencing. De novo assembly yielded 2934 metagenome-assembled genomes (MAGs). Profiling revealed significant enrichment of Parabacteroides distasonis and Bacteroides thetaiotaomicron after the intervention, with inverse correlations between their relative abundances and parameters related to obesity and atherosclerotic cardiovascular diseases (ASCVD). MAGs enriched after the intervention showed high richness and diversity of carbohydrate-active enzymes, with an increased relative abundances of genes related to succinate production and glutamate fermentation.
Keywords	Microbial ecology ; QR100-130
Subject code	796
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The genomic landscape of reference genomes of cultivated human gut bacteria

Xiaoqian Lin / Tongyuan Hu / Jianwei Chen / Hewei Liang / Jianwei Zhou / Zhinan Wu / Chen Ye / Xin Jin / Xun Xu / Wenwei Zhang / Xiaohuan Jing / Tao Yang / Jian Wang / Huanming Yang / Karsten Kristiansen / Liang Xiao / Yuanqiang Zou

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 11

Abstract: Here, the authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, a catalog that includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals, and classifies 527 species from 8 phyla, ...

Abstract	Here, the authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, a catalog that includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals, and classifies 527 species from 8 phyla, including 179 previously unidentified species, and provides information of secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.
Keywords	Science ; Q
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A catalog of bacterial reference genomes from cultivated human oral bacteria

Wenxi Li / Hewei Liang / Xiaoqian Lin / Tongyuan Hu / Zhinan Wu / Wenxin He / Mengmeng Wang / Jiahao Zhang / Zhuye Jie / Xin Jin / Xun Xu / Jian Wang / Huanming Yang / Wenwei Zhang / Karsten Kristiansen / Liang Xiao / Yuanqiang Zou

npj Biofilms and Microbiomes, Vol 9, Iss 1, Pp 1-

2023 Volume 13

Abstract: Abstract The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality ... ...

Abstract	Abstract The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.
Keywords	Microbial ecology ; QR100-130
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: IgG and IgM cooperate in coating of intestinal bacteria in IgA deficiency

Carsten Eriksen / Janne Marie Moll / Pernille Neve Myers / Ana Rosa Almeida Pinto / Niels Banhos Danneskiold-Samsøe / Rasmus Ibsen Dehli / Lisbeth Buus Rosholm / Marlene Danner Dalgaard / John Penders / Daisy MAE Jonkers / Qiang Pan-Hammarström / Lennart Hammarström / Karsten Kristiansen / Susanne Brix

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Immunoglobulin A (IgA) is acknowledged to play a role in the defence of the mucosal barrier by coating microorganisms. Surprisingly, IgA-deficient humans exhibit few infection-related complications, raising the question if the more specific IgG ... ...

Abstract	Abstract Immunoglobulin A (IgA) is acknowledged to play a role in the defence of the mucosal barrier by coating microorganisms. Surprisingly, IgA-deficient humans exhibit few infection-related complications, raising the question if the more specific IgG may help IgM in compensating for the lack of IgA. Here we employ a cohort of IgA-deficient humans, each paired with IgA-sufficient household members, to investigate multi-Ig bacterial coating. In IgA-deficient humans, IgM alone, and together with IgG, recapitulate coating of most bacterial families, despite an overall 3.6-fold lower Ig-coating. Bacterial IgG coating is dominated by IgG1 and IgG4. Single-IgG2 bacterial coating is sparse and linked to enhanced Escherichia coli load and TNF-α. Although single-IgG2 coating is 1.6-fold more prevalent in IgA deficiency than in healthy controls, it is 2-fold less prevalent than in inflammatory bowel disease. Altogether we demonstrate that IgG assists IgM in coating of most bacterial families in the absence of IgA and identify single-IgG2 bacterial coating as an inflammatory marker.
Keywords	Science ; Q
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq

Tu Hu / Tanja Todberg / Daniel Andersen / Niels Banhos Danneskiold-Samsøe / Sofie Boesgaard Neestrup Hansen / Karsten Kristiansen / David Adrian Ewald / Susanne Brix / Joel Correa da Rosa / Ilka Hoof / Lone Skov / Thomas Litman

International Journal of Molecular Sciences, Vol 23, Iss 6140, p

2022 Volume 6140

Abstract: Tape stripping is a non-invasive skin sampling technique, which has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated ... ...

Abstract	Tape stripping is a non-invasive skin sampling technique, which has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated immune response. Here, we performed BRB-seq—a low cost, multiplex-based, transcriptomic profiling technique—on tape-stripped skin from 30 AD patients and 30 healthy controls to evaluate the methods’ ability to assess the epidermal AD transcriptome. An AD signature consisting of 91 differentially expressed genes, specific for skin barrier and inflammatory response, was identified. The gene expression in the outermost layers, stratum corneum and stratum granulosum, of the skin showed highest correlation between tape-stripped skin and matched full-thickness punch biopsies. However, we observed that low and highly variable transcript counts, probably due to low RNA yield and RNA degradation in the tape-stripped skin samples, were a limiting factor for epidermal transcriptome profiling as compared to punch biopsies. We conclude that deep BRB-seq of tape-stripped skin is needed to counteract large between-sample RNA yield variation and highly zero-inflated data in order to apply this protocol for population-wide screening of the epidermal transcriptome in inflammatory skin diseases.
Keywords	tape stripping ; atopic dermatitis ; epidermis ; transcriptome ; BRB-seq ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	571
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen / Kasper Rømer Villumsen / Madeleine Ernst / Martin Hansen / Torunn Forberg / Shyam Gopalakrishnan / M. Thomas P. Gilbert / Anders Miki Bojesen / Karsten Kristiansen / Morten Tønsberg Limborg

Microbiome, Vol 10, Iss 1, Pp 1-

2022 Volume 19

Abstract: Abstract Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the ... ...

Abstract	Abstract Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism. Results Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites. Conclusion Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract
Keywords	Microbial ecology ; QR100-130
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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