Publications by authors named "Daniel Huson"

90 Publications

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing.

NPJ Biofilms Microbiomes 2021 03 16;7(1):23. Epub 2021 Mar 16.

Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
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http://dx.doi.org/10.1038/s41522-021-00196-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7966762PMC
March 2021

DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences.

Curr Protoc 2021 Mar;1(3):e59

Institute of Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.

One main approach to computational analysis of microbiome sequences is to first align against a reference database of annotated protein sequences (NCBI-nr) and then perform taxonomic and functional binning of the sequences based on the resulting alignments. For both short and long reads (or assembled contigs), alignment is performed using DIAMOND, whereas taxonomic and functional binning, followed by inter- active exploration and analysis, is performed using MEGAN. We provide two step-by-step descriptions of this approach: © 2021 The Authors. Basic Protocol 1: Taxonomic and functional analysis of short read microbiome sequences Support Protocol 1: Preprocessing Basic Protocol 2: taxonomic and functional analysis of assembled long read microbiome sequences Support Protocol 2: Taxonomic binning and CheckM.
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http://dx.doi.org/10.1002/cpz1.59DOI Listing
March 2021

The Isolate sp. 7D4C2 Produces -Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria.

Front Microbiol 2020 14;11:594524. Epub 2021 Jan 14.

AG Angenent, Max Planck Institute for Developmental Biology, Max Planck Society (MPG), Tübingen, Germany.

Bulk production of medium-chain carboxylates (MCCs) with 6-12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors. When in-line MCC extraction and prevention of product inhibition is required, the bioreactors have been operated at mildly acidic pH (5.0-5.5). However, model chain-elongating bacteria grow optimally at neutral pH values. Here, we isolated a chain-elongating bacterium (strain 7D4C2) that grows at mildly acidic pH. We studied its metabolism and compared its whole genome and the reverse β-oxidation (rBOX) genes to other bacteria. Strain 7D4C2 produces lactate, acetate, -butyrate, -caproate, biomass, and H/CO from hexoses. With only fructose as substrate (pH 5.5), the maximum -caproate specificity (i.e., products other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and -butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and -butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing -caproate specificity from ∼92% at mildly acidic pH (pH 4.5-5.0) to ∼24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated -caproic acid was ∼0.3 mM), the -caproate selectivity (i.e., product substrate fed) was 42.6 ± 19.0% higher compared to 7D4C2 cultures without extraction. Based on the 16S rRNA gene sequence, strain 7D4C2 is most closely related to the isolates (99.5%) and (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, , and belong to the same genus of . Their rBOX genes are conserved and located next to each other, forming a gene cluster, which is different than for other chain-elongating bacteria such as spp. In conclusion, spp., comprising strain 7D4C2, , , and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. sp. 7D4C2 (DSM 110548) was studied here to understand -caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into -caproate.
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http://dx.doi.org/10.3389/fmicb.2020.594524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873966PMC
January 2021

The structure of autocatalytic networks, with application to early biochemistry.

J R Soc Interface 2020 10 7;17(171):20200488. Epub 2020 Oct 7.

Center for Bioinformatics, University of Tübingen, Tubingen, Germany.

Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronized fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organization of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualize RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide techniques to study and visualize the core aspects of primitive biochemistry.
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http://dx.doi.org/10.1098/rsif.2020.0488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653369PMC
October 2020

MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.

BMC Bioinformatics 2020 Sep 17;21(Suppl 13):390. Epub 2020 Sep 17.

Department of Computer Science, University of Tübingen, Sand 14, Tübingen, Germany.

Background: Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud.

Results: MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

Conclusions: We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.
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http://dx.doi.org/10.1186/s12859-020-03684-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495841PMC
September 2020

Methylation of CpG 5962 in L1 of the human papillomavirus 16 genome as a potential predictive marker for viral persistence: A prospective large cohort study using cervical swab samples.

Cancer Med 2020 02 19;9(3):1058-1068. Epub 2019 Dec 19.

Medical Virology, Institute of Medical Virology, University Hospital of Tuebingen, Tuebingen, Germany.

Several studies have demonstrated that the viral genome can be methylated by the host cell during progression from persistent infection to cervical cancer. The aim of this study was to investigate whether methylation at a specific site could predict the development of viral persistence and whether viral load shows a correlation with specific methylation patterns. HPV16-positive samples from women aged 20-29 years (n = 99) with a follow-up time of 13 years, were included from a Danish cohort comprising 11 088 women. Viral load was measured by real-time PCR and methylation status was determined for 39 CpG sites in the upstream regulatory region (URR), E6/E7, and L1 region of HPV16 by next-generation sequencing. Participants were divided into two groups according to whether they were persistently (≥ 24 months) or transiently HPV16 infected. The general methylation status was significantly different between women with a persistent and women with a transient infection outcome (P = .025). One site located in L1 (nt. 5962) was statistically significantly (P = .00048) different in the methylation status after correction using the Holm-Sidak method (alpha = 0.05). Correlation analyses of samples from HPV16 persistently infected women suggest that methylation is higher although viral load is lower. This study indicates that methylation at position 5962 of the HPV16 genome within the L1 gene might be a predictive marker for the development of a persistent HPV16 infection.
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http://dx.doi.org/10.1002/cam4.2771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997067PMC
February 2020

Enriched Environmental Conditions Modify the Gut Microbiome Composition and Fecal Markers of Inflammation in Parkinson's Disease.

Front Neurosci 2019 15;13:1032. Epub 2019 Oct 15.

Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.

Recent findings suggest an implication of the gut microbiome in Parkinson's disease (PD) patients. PD onset and progression has also been linked with various environmental factors such as physical activity, exposure to pesticides, head injury, nicotine, and dietary factors. In this study, we used a mouse model, overexpressing the complete human SNCA gene (SNCA-TG mice) modeling familial and sporadic forms of PD to study whether environmental conditions such as standard enriched environment changes the gut microbiome and influences disease progression. We performed 16S rRNA DNA sequencing on fecal samples for microbiome analysis and studied fecal inflammatory calprotectin from the colon of control and SNCA-TG mice kept under standard environment (SE) and enriched environment (EE) conditions. The overall composition of the gut microbiota was not changed in SNCA-TG mice compared with WT in EE with respect to SE. However, individual gut bacteria at genus level such as sp. was a significant changed in the SNCA-TG mice. EE significantly reduced colon fecal inflammatory calprotectin protein in WT and SNCA-TG EE compared to SE. Moreover, EE reduces the pro-inflammatory cytokines in the feces and inflammation inducing genes in the colon. Our data suggest that an enriched social environment has a positive effect on the induction of SNCA mediated inflammation in the intestine and by modulating anti-inflammatory gut bacteria.
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http://dx.doi.org/10.3389/fnins.2019.01032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842954PMC
October 2019

Phage tail-like particles are versatile bacterial nanomachines - A mini-review.

J Adv Res 2019 Sep 23;19:75-84. Epub 2019 Apr 23.

Institute for National and International Plant Health, Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany.

Type VI secretion systems and tailocins, two bacterial phage tail-like particles, have been reported to foster interbacterial competition. Both nanostructures enable their producer to kill other bacteria competing for the same ecological niche. Previously, type VI secretion systems and particularly R-type tailocins were considered highly specific, attacking a rather small range of competitors. Their specificity is conferred by cell surface receptors of the target bacterium and receptor-binding proteins on tailocin tail fibers and tail fiber-like appendages of T6SS. Since many R-type tailocin gene clusters contain only one tail fiber gene it was appropriate to expect small R-type tailocin target ranges. However, recently up to three tail fiber genes and broader target ranges have been reported for one plant-associated strain. Here, we show that having three tail fiber genes per R-type tailocin gene cluster is a common feature of several strains of Gram-negative (often plant-associated) bacteria of the genus . Knowledge about the specificity of type VI secretion systems binding to target bacteria is even lower than in R-type tailocins. Although the mode of operation implicated specific binding, it was only published recently that type VI secretion systems develop tail fiber-like appendages. Here again , exhibiting up to three different type VI secretion systems, may provide valuable insights into the antagonistic potential of plant-associated bacteria. Current understanding of the diversity and potential of phage tail-like particles is fragmentary due to various synonyms and misleading terminology. Consistency in technical terms is a precondition for concerted and purposeful research, which precedes a comprehensive understanding of the specific interaction between bacteria producing phage tail-like particles and their targets. This knowledge is fundamental for selecting and applying tailored, and possibly engineered, producer bacteria for antagonizing plant pathogenic microorganisms.
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http://dx.doi.org/10.1016/j.jare.2019.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629978PMC
September 2019

Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.

Methods Mol Biol 2019 ;1910:591-604

Algorithms in Bioinformatics, Faculty of Computer Science, University of Tübingen, Tübingen, Germany.

Metagenomics has become a part of the standard toolkit for scientists interested in studying microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse taxonomic profiling of samples, shotgun metagenomic sequencing provides a more detailed analysis of the taxonomic and functional content of samples. Long read technologies, such as developed by Pacific Biosciences or Oxford Nanopore, produce much longer stretches of informative sequence, greatly simplifying the difficult and time-consuming process of metagenomic assembly. MEGAN6 provides a wide range of analysis and visualization methods for the analysis of short and long read metagenomic data. A simple and efficient analysis pipeline for metagenomic analysis consists of the DIAMOND alignment tool on short reads, or the LAST alignment tool on long reads, followed by MEGAN. This approach performs taxonomic and functional abundance analysis, supports comparative analysis of large-scale experiments, and allows one to involve experimental metadata in the analysis.
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http://dx.doi.org/10.1007/978-1-4939-9074-0_19DOI Listing
January 2020

Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.

Cell Host Microbe 2019 05 18;25(5):681-694.e8. Epub 2019 Apr 18.

Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, 80336 Munich, Germany. Electronic address:

The microbiota and the gastrointestinal mucus layer play a pivotal role in protection against non-typhoidal Salmonella enterica serovar Typhimurium (S. Tm) colitis. Here, we analyzed the course of Salmonella colitis in mice lacking a functional mucus layer in the gut. Unexpectedly, in contrast to mucus-proficient littermates, genetically deficient mice were protected against Salmonella-induced gut inflammation in the streptomycin colitis model. This correlated with microbiota alterations and enrichment of the bacterial phylum Deferribacteres. Using gnotobiotic mice associated with defined bacterial consortia, we causally linked Mucispirillum schaedleri, currently the sole known representative of Deferribacteres present in the mammalian microbiota, to host protection against S. Tm colitis. Inhibition by M. schaedleri involves interference with S. Tm invasion gene expression, partly by competing for anaerobic electron acceptors. In conclusion, this study establishes M. schaedleri, a core member of the murine gut microbiota, as a key antagonist of S. Tm virulence in the gut.
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http://dx.doi.org/10.1016/j.chom.2019.03.004DOI Listing
May 2019

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.

Microbiome 2019 04 16;7(1):61. Epub 2019 Apr 16.

Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

Background: Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.

Results: We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts.

Conclusions: Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.
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http://dx.doi.org/10.1186/s40168-019-0665-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469205PMC
April 2019

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.

Cell Host Microbe 2019 Apr;25(4):553-564.e7

Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. Electronic address:

Host genetic variation influences microbiome composition. While studies have focused on associations between the gut microbiome and specific alleles, gene copy number (CN) also varies. We relate microbiome diversity to CN variation of the AMY1 locus, which encodes salivary amylase, facilitating starch digestion. After imputing AMY1-CN for ∼1,000 subjects, we identified taxa differentiating fecal microbiomes of high and low AMY1-CN hosts. In a month-long diet intervention study, we show that diet standardization drove gut microbiome convergence, and AMY1-CN correlated with oral and gut microbiome composition and function. The microbiomes of low-AMY1-CN subjects had enhanced capacity to break down complex carbohydrates. High-AMY1-CN subjects had higher levels of salivary Porphyromonas; their gut microbiota had increased abundance of resistant starch-degrading microbes, produced higher levels of short-chain fatty acids, and drove higher adiposity when transferred to germ-free mice. This study establishes AMY1-CN as a genetic factor associated with microbiome composition and function.
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http://dx.doi.org/10.1016/j.chom.2019.03.001DOI Listing
April 2019

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.

Biol Direct 2018 04 20;13(1). Epub 2018 Apr 20.

Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

Background: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets.

Methods: We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods.

Results: All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.

Reviewers: This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul.

Conclusion: This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.
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http://dx.doi.org/10.1186/s13062-018-0208-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5910613PMC
April 2018

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico.

Nat Ecol Evol 2018 03 15;2(3):520-528. Epub 2018 Jan 15.

Max Planck Institute for the Science of Human History, Jena, Germany.

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.
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http://dx.doi.org/10.1038/s41559-017-0446-6DOI Listing
March 2018

Genome Sequence of (Greater Wax Moth).

Genome Announc 2018 Jan 11;6(2). Epub 2018 Jan 11.

Department for Medical Microbiology and Hygiene, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany

The larvae of the greater wax moth, , are pests of active beehives. In infection biology, these larvae are playing a more and more attractive role as an invertebrate host model. Here, we report on the first genome sequence of .
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http://dx.doi.org/10.1128/genomeA.01220-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764926PMC
January 2018

Soil biochar amendment affects the diversity of nosZ transcripts: Implications for NO formation.

Sci Rep 2017 06 13;7(1):3338. Epub 2017 Jun 13.

Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, 55455, MN, USA.

Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (NO). Soil biochar amendment has been shown to significantly decrease NO emissions in various soils. However, the effect of biochar on the structure and function of microbial communities that actively perform nitrogen redox transformations has not been studied in detail yet. To analyse the community composition of actively denitrifying and NO-reducing microbial communities, we collected RNA samples at different time points from a soil microcosm experiment conducted under denitrifying conditions and performed Illumina amplicon sequencing targeting nirK, typical nosZ and atypical nosZ mRNA transcripts. Within 10 days, biochar significantly increased the diversity of nirK and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing microbial community. Furthermore, biochar addition led to a significant increase in transcript production among microbial species that are specialized on direct NO reduction from the environment. Our results point towards a potential coupling of biochar-induced NO emission reduction and an increase in microbial NO reduction activity among specific groups of typical and atypical NO reducers. However, experiments with other soils and biochars will be required to verify the transferability of these findings to other soil-biochar systems.
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http://dx.doi.org/10.1038/s41598-017-03282-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5469825PMC
June 2017

Soil biochar amendment affects the diversity of nosZ transcripts: Implications for NO formation.

Sci Rep 2017 06 13;7(1):3338. Epub 2017 Jun 13.

Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, 55455, MN, USA.

Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (NO). Soil biochar amendment has been shown to significantly decrease NO emissions in various soils. However, the effect of biochar on the structure and function of microbial communities that actively perform nitrogen redox transformations has not been studied in detail yet. To analyse the community composition of actively denitrifying and NO-reducing microbial communities, we collected RNA samples at different time points from a soil microcosm experiment conducted under denitrifying conditions and performed Illumina amplicon sequencing targeting nirK, typical nosZ and atypical nosZ mRNA transcripts. Within 10 days, biochar significantly increased the diversity of nirK and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing microbial community. Furthermore, biochar addition led to a significant increase in transcript production among microbial species that are specialized on direct NO reduction from the environment. Our results point towards a potential coupling of biochar-induced NO emission reduction and an increase in microbial NO reduction activity among specific groups of typical and atypical NO reducers. However, experiments with other soils and biochars will be required to verify the transferability of these findings to other soil-biochar systems.
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http://dx.doi.org/10.1038/s41598-017-03282-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5469825PMC
June 2017

SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?

BMC Genomics 2017 03 14;18(Suppl 2):114. Epub 2017 Mar 14.

University of Tübingen, Department of Computer Science, Sand 14, Tübingen, 72076, Germany.

Background: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies.

Results: We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT).

Conclusions: While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic.
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http://dx.doi.org/10.1186/s12864-017-3501-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374703PMC
March 2017

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Nature 2017 04 8;544(7650):357-361. Epub 2017 Mar 8.

Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK.

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.
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http://dx.doi.org/10.1038/nature21674DOI Listing
April 2017

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.

BMC Bioinformatics 2016 Dec 22;17(Suppl 19):508. Epub 2016 Dec 22.

Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore.

Background: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.

Results: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.

Conclusions: RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.
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http://dx.doi.org/10.1186/s12859-016-1378-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259810PMC
December 2016

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Microbiome 2017 01 25;5(1):11. Epub 2017 Jan 25.

Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

Background: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes.

Methods: We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled.

Results: Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered.

Conclusions: Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.
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http://dx.doi.org/10.1186/s40168-017-0233-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5267372PMC
January 2017

A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples.

J Biotechnol 2017 May 27;250:45-50. Epub 2016 Oct 27.

Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany; German Center for Infection Research (DZIF), Partner Site Tübingen, Germany.

One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical "triangulation test" to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples. To illustrate the application of the test, we collected three biological samples taken from different locations in one piece of human stool, each represented by three replicates, and analyzed them using MEGAN. (Despite its name, the triangulation test does not require that the number of biological samples or replicates be three.) The triangulation test rejects the null hypothesis that the three biological samples exhibit the same distribution of taxa or function (error probability ≤0.05), indicating that the microbial composition of the investigated human stool is not homogenous on a macroscopic scale, suggesting that pooling material from multiple locations is a reasonable practice. We provide an implementation of the test in our open source program MEGAN Community Edition.
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http://dx.doi.org/10.1016/j.jbiotec.2016.10.020DOI Listing
May 2017

Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2).

PLoS One 2016 8;11(12):e0168035. Epub 2016 Dec 8.

Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain.

In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168035PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5145203PMC
July 2017

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.

Nat Microbiol 2016 Nov 21;2:16215. Epub 2016 Nov 21.

Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany.

Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe-microbe and microbe-host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.
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http://dx.doi.org/10.1038/nmicrobiol.2016.215DOI Listing
November 2016

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil.

Sci Rep 2016 06 29;6:28958. Epub 2016 Jun 29.

Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, MN, USA.

In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas. We detected a so far unknown diversity of genes encoding for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases as well as metabolic and cometabolic dehalogenases. Genes for non-heme, no-metal chloroperoxidases and haloalkane dehalogenases were the most abundant halogenase and dehalogenase genes, respectively. The high diversity and abundance of (de)halogenating enzymes suggests a strong microbial contribution to natural halogen cycling. This was also confirmed in microcosm experiments in which we quantified the biotic formation of chloroform and bromoform. Knowledge on microorganisms and genes that catalyze (de)halogenation reactions is critical because they are highly relevant to industrial biotechnologies and bioremediation applications.
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http://dx.doi.org/10.1038/srep28958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926216PMC
June 2016

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

PLoS Comput Biol 2016 06 21;12(6):e1004957. Epub 2016 Jun 21.

Center for Bioinformatics, University of Tübingen, Tübingen, Germany.

There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.
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http://dx.doi.org/10.1371/journal.pcbi.1004957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915700PMC
June 2016

Intestinal Dysbiosis, Barrier Dysfunction, and Bacterial Translocation Account for CKD-Related Systemic Inflammation.

J Am Soc Nephrol 2017 Jan 5;28(1):76-83. Epub 2016 May 5.

Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität and

CKD associates with systemic inflammation, but the underlying cause is unknown. Here, we investigated the involvement of intestinal microbiota. We report that collagen type 4 α3-deficient mice with Alport syndrome-related progressive CKD displayed systemic inflammation, including increased plasma levels of pentraxin-2 and activated antigen-presenting cells, CD4 and CD8 T cells, and Th17- or IFNγ-producing T cells in the spleen as well as regulatory T cell suppression. CKD-related systemic inflammation in these mice associated with intestinal dysbiosis of proteobacterial blooms, translocation of living bacteria across the intestinal barrier into the liver, and increased serum levels of bacterial endotoxin. Uremia did not affect secretory IgA release into the ileum lumen or mucosal leukocyte subsets. To test for causation between dysbiosis and systemic inflammation in CKD, we eradicated facultative anaerobic microbiota with antibiotics. This eradication prevented bacterial translocation, significantly reduced serum endotoxin levels, and fully reversed all markers of systemic inflammation to the level of nonuremic controls. Therefore, we conclude that uremia associates with intestinal dysbiosis, intestinal barrier dysfunction, and bacterial translocation, which trigger the state of persistent systemic inflammation in CKD. Uremic dysbiosis and intestinal barrier dysfunction may be novel therapeutic targets for intervention to suppress CKD-related systemic inflammation and its consequences.
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http://dx.doi.org/10.1681/ASN.2015111285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198279PMC
January 2017

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

Sci Total Environ 2016 08 18;562:379-390. Epub 2016 Apr 18.

Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen, Germany; Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116, USA; BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106, USA. Electronic address:

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling.
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http://dx.doi.org/10.1016/j.scitotenv.2016.03.220DOI Listing
August 2016

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.

Genome Biol Evol 2016 Apr 25;8(4):1197-207. Epub 2016 Apr 25.

Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany

Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.
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http://dx.doi.org/10.1093/gbe/evw070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860699PMC
April 2016