Li Deng

Li Deng
Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) | HZM

About

84
Publications
12,245
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,423
Citations

Publications

Publications (84)
Preprint
OBJECTIVE H. pylori infection is the most prevalent bacterial infection worldwide. Besides being the most important risk factor for gastric cancer development, epidemiological data show that infected individuals harbor a nearly two-fold increased risk to develop colorectal cancer (CRC). However, a direct causal and functional connection between H....
Article
The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In add...
Article
Full-text available
Despite the growing interest in the microbiome in recent years, the study of the virome, the major part of which is made up of bacteriophages, is relatively underdeveloped compared with their bacterial counterparts. This is due in part to the lack of a universally conserved marker such as the 16S rRNA gene. For this reason, the development of metag...
Article
Full-text available
The acquisition and development of the mammalian microbiome early in life are critical to establish a healthy host-microbiome symbiosis. Despite recent advances in understanding microbial sources in infants, the relative contribution of various microbial sources to the colonization of the gut microbiota in pigs remains unclear. Here, we longitudina...
Preprint
The intestinal bacteriome directly affects outcome in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-SCT). Besides bacteria, fungal and viral communities as well as microbiota-derived metabolites play a role. Yet, it is still unclear how dynamic shifts in these three communities contribute to (1) clinical outcome of al...
Article
The intestinal microbiome directly effects outcomes in patients undergoing allogeneic stem cell transplantation (ASCT) (Peled et al., N Engl J Med, 2020). Recent developments in microbiome research allow us to look beyond bacterial communities at the composition of the intestinal mycobiome and virome. However, only few studies have addressed these...
Article
Full-text available
The relationship between viruses (dominated by bacteriophages or phages) and lower gastrointestinal (GI) tract diseases has been investigated, whereas the relationship between gut bacteriophages and upper GI tract diseases, such as esophageal diseases, which mainly include Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC), remains poorly...
Article
Full-text available
Gut bacteria play an essential role in the human body by regulating multiple functions, producing essential metabolites, protecting against pathogen invasion, and much more. Conversely, changes in their community structure are linked to several gastrointestinal (GI) and non-GI conditions. Fortunately, these bacteria are amenable to external perturb...
Article
The control of degrader populations and the stochasticity and certainty of the microbial community in contaminated groundwater are not well-understood. In this study, a long-term contaminated groundwater ecosystem was selected to investigate the impact of BTEX on microbial communities and how microbial communities respond to BTEX pollution. 16 S rR...
Article
Full-text available
We are surrounded by microbes, mostly bacteria and their viruses or phages, on the inside and outside of our bodies. These bacteria in constant interactions with phages are regulating multiple functions critical to our health. Luckily, they are amenable, but we need precise tools for their safe manipulation and improving human health. Here, we argu...
Article
Full-text available
Determining exact viral titers in a given sample is essential for many environmental and clinical applications, e.g., for studying viral ecology or application of bacteriophages for food safety. However, virus quantification is not a simple task, especially for complex environmental samples. While clonal viral isolates can be quantified with relati...
Preprint
Full-text available
Background: The acquisition and development of the mammalian microbiome early in life are critical to establish a healthy host-microbiome symbiosis. The maternal and environmental microbial reservoirs are considered the main sources of microbial communities in newborn mammals. However, the timely relative contribution of various microbial sources t...
Article
Full-text available
In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present expe...
Article
Full-text available
Harmful algal blooms formed by colony-forming cyanobacteria deteriorate water resources by producing cyanotoxins, which frequently occur at high intracellular concentrations. We aimed to localize toxic microcystins (MCs) and bioactive anabaenopeptins (APs) at the subcellular level under noninvasive conditions. Since both metabolites are synthesized...
Article
Full-text available
Stunting, a severe and multigenerational growth impairment, globally affects 22% of children under the age of 5 years. Stunted children have altered gut bacterial communities with higher proportions of Proteobacteria, a phylum with several known human pathogens. Despite the links between an altered gut microbiota and stunting, the role of bacteriop...
Article
Full-text available
The disturbing effect of a short-term cooling period during summer on planktonic bacterial community structure of an alpine lake was investigated using 16S rDNA pyrosequencing. Proteobacteria, Actinobacteria, and Bacteroidetes constituted the most abundant phyla. During the sampling period (from July to August 2010), a sudden cooling period with hi...
Article
Full-text available
Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-base...
Article
Full-text available
Alpine lakes are considered pristine freshwater ecosystems and sensitive to direct and indirect changes in water temperature as induced by climate change. The bacterial plankton constitutes a key component in the water column and bacterial metabolic activity has direct consequences for water quality. In order to understand bacterial response to glo...
Article
Full-text available
Background With the advent of the age of big data in bioinformatics, large volumes of data and high performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing techno...
Data
Venn diagram showing the number of shared HVPC clusters between the three BAL samples.
Data
Blast results for BAL sequences vs the core Viruelence Factors Database.
Data
Rarefaction curves showing the number of Human Virome Protein Cluster (HVPC) hits versus sample size based on random subsampling and a step size of 50 sequences.
Data
Metadata of downloaded virome datasets.
Data
The flexible virome of COPD samples.
Data
Heat map showing the relative abundance of 36 prokaryotic viruses shared between the three BAL samples.
Data
Heat map showing the relative abundance of 15 eukaryotic viruses shared between the three BAL samples.
Data
Rarefaction curves showing the number of species versus sample size based on random subsampling and a step size of 50 sequences.
Data
Functional annotation of the representative ORFs of the core human virome clusters.
Data
Basic statistics of downloaded metageomes before and after quality control.
Article
Despite the recognized excellence of virology and bioinformatics, these two communities have interacted surprisingly sporadically, aside from some pioneering work on HIV-1 and influenza. Bringing together the expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for viru...
Article
Full-text available
Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually...
Preprint
Full-text available
Background With the advent of the age of big data in bioinformatics, large volumes of data and high performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing techno...
Article
Full-text available
Despite the active and intense treatment of wastewater, pathogenic microorganisms and viruses are frequently introduced into the aquatic environment. For most human pathogens, however, this is a rather hostile place, where starvation, continuous inactivation, and decay generally occur, rather than successful reproduction. Nevertheless, a great dive...
Chapter
With fast development and wide applications of next generation sequencing (NGS) technologies, pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the microbial community profiles. In this chapter we describe an approach for sequencing 16S rRNA gene amplic...
Article
Full-text available
Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the prese...
Article
Full-text available
Bloom-forming cyanobacteria Planktothrix agardhii and P. rubescens are regularly involved in the occurrence of cyanotoxin in lakes and reservoirs. Besides microcystins (MCs), which inhibit eukaryotic protein phosphatase 1 and 2A, several families of bioactive peptides are produced, thereby resulting in impressive secondary metabolite structural div...
Article
Full-text available
Background Bloom-forming cyanobacteria cause toxic algae outbreaks in lakes and reservoirs. We aimed to explore and quantify mutation events occurring within the large mcy gene cluster (55 kbp) encoding microcystin (MC) biosynthesis that inactivate MC net production. For this purpose we developed a workflow to detect mutations in situ occurring any...
Article
Ocean viruses are abundant, ubiquitous, and play important roles in global biogeochemical cycles through mortality, horizontal gene transfer and manipulation of host metabolism. However, the ability to link viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. Here,...
Article
Full-text available
Toxic freshwater cyanobacteria form harmful algal blooms that can cause acute toxicity to humans and livestock. Globally distributed, bloom-forming cyanobacteria Planktothrix either retain or lose the mcy gene cluster (encoding the synthesis of the secondary metabolite hepatotoxin microcystin or MC), resulting in a variable spatial/temporal distrib...
Article
Full-text available
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated vir...
Article
The trophic interactions between viruses, bacteria and protists play a crucial role in structuring microbial communities and regulating nutrient and organic matter flux. Here, we show that the impact on viral density by heterotrophic flagellates is related to their feeding behaviour (feeding on sedimented particles – Thaumatomonas coloniensis, filt...
Article
Full-text available
Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in...
Data
Supplemental materials and methods. Download Text S1, DOCX file, 0.1 MB.
Data
Schematic overview of VT staining optimizations: three dyes (SYBR gold, SYBR green II, and SYBR Safe) were compared under various incubation conditions (80°C for 10 min, room temperature for 10 min, and 4°C for overnight) to identify the optimal VT conditions. All experiments were conducted with the cyanomyovirus Syn33 and the host strain Synechoco...
Data
Adsorption kinetic experiments of Pseudoalteromonas siphovirus PSA-HS6 against four Pseudoalteromonas strains revealed that this siphovirus adsorbs to all four strains. As inferred from traditional plaque and liquid infection assays, this siphovirus infects two of these cell strains (host; solid lines), 11-68 and 13-15, but not the other two (nonho...
Data
Recovery rate of viruses (cyanomyoviruses Syn33 and S-SM1; Pseudoalteromonas viruses myovirus PSA-HM3, podovirus PSA-HP1, and siphovirus PSA-HS4) using ultracentrifugal devices (Nanosep with low-protein-binding membranes; Pall, New York, NY) with a 10,000 or 100,000 molecular weight cutoff (MWCO) under various conditions. Treatments include pretrea...
Data
Percentage of Synechococcus WH7803 cells tagged by phage Syn33 using VT at a VBR of 10 at 0, 30, 60, and 120 min after mixture of bacteria and viruses. Each test was done in triplicate (error bars show standard deviations) at concentrations of 106 cells ml−1. Download Figure S5, DOCX file, 0.1 MB.
Data
Comparison of fluorescence-based and flow cytometry (FCM) cell count-based growth curves of photoautotrophic Synechococcus strain WH7803. Download Figure S6, DOCX file, 0.1 MB.
Data
PFU of SYBR gold-labeled (80°C, 10 min) viruses and unlabeled ones on their host lawns. Each test was done in triplicate (error bars show standard deviations). Download Figure S2, DOCX file, 0.1 MB.