Joerg Graf
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View article: The role of co-infection in the pathogenesis of acute SARS-CoV-2 infection and development of post-acute sequelae: A perspective
The role of co-infection in the pathogenesis of acute SARS-CoV-2 infection and development of post-acute sequelae: A perspective Open
A major health challenge resulting from the COVID-19 pandemic is the manifestation of post-acute sequelae of SARS-CoV-2 (PASC). PASC (or long COVID) is a collective term used for clinical symptoms, various pathologies, and life-quality-cha…
View article: Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis
Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis Open
Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina’s platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long read seq…
View article: Identification and characterization of the surface layer protein AvsA in outer membrane vesicles, antibiotic resistance, and <i>in vivo</i> host colonization in <i>Aeromonas veronii</i>
Identification and characterization of the surface layer protein AvsA in outer membrane vesicles, antibiotic resistance, and <i>in vivo</i> host colonization in <i>Aeromonas veronii</i> Open
Outer membrane vesicles (OMVs) are important in bacterial communication and the transfer of virulence factors. In this study, we identified and characterized the surface layer protein (SLP) AvsA ( A eromonas v eronii s urface protein A ) i…
View article: Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes
Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes Open
Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing nonhomologous genes) or repla…
View article: Slowing Alzheimer’s disease progression through probiotic supplementation
Slowing Alzheimer’s disease progression through probiotic supplementation Open
The lack of affordable and effective therapeutics against cognitive impairment has promoted research toward alternative approaches to the treatment of neurodegeneration. In recent years, a bidirectional pathway that allows the gut to commu…
View article: Editorial: Microbial associates of blood-sucking arthropods and other animals: relevance to their physiology, ecology and evolution
Editorial: Microbial associates of blood-sucking arthropods and other animals: relevance to their physiology, ecology and evolution Open
International audience
View article: Development of a biomarker signature using grating-coupled fluorescence plasmonic microarray for diagnosis of MIS-C
Development of a biomarker signature using grating-coupled fluorescence plasmonic microarray for diagnosis of MIS-C Open
Multisystem inflammatory syndrome in children (MIS-C) is a rare but serious condition that can develop 4–6 weeks after a school age child becomes infected by SARS-CoV-2. To date, in the United States more than 8,862 cases of MIS-C have bee…
View article: Draft Genome Sequence of Plesiomonas shigelloides MD22D9, Isolated from the Digestive Tract of Macrobdella decora
Draft Genome Sequence of Plesiomonas shigelloides MD22D9, Isolated from the Digestive Tract of Macrobdella decora Open
Here, we present a draft genome sequence of Plesiomonas shigelloides MD22D9, isolated from the digestive tract of the North American medicinal leech Macrobdella decora . The gut microbiome of the medicinal leech is hypothesized to be criti…
View article: <i>Pseudomonas apudapuas</i>sp. nov.,<i>Pseudomonas fontis</i>sp. nov.,<i>Pseudomonas idahonensis</i>sp. nov., and<i>Pseudomonas rubra</i>sp. nov. isolated from in, and around, a rainbow trout farm
<i>Pseudomonas apudapuas</i>sp. nov.,<i>Pseudomonas fontis</i>sp. nov.,<i>Pseudomonas idahonensis</i>sp. nov., and<i>Pseudomonas rubra</i>sp. nov. isolated from in, and around, a rainbow trout farm Open
During a large-scale bacterial culturing effort of biofilms in the vicinity of a rainbow trout aquaculture facility in Idaho, USA, ten isolates were identified as having pathogen inhibiting activity and were characterized further. These is…
View article: Large-Scale, Multi-Year Microbial Community Survey of a Freshwater Trout Aquaculture Facility
Large-Scale, Multi-Year Microbial Community Survey of a Freshwater Trout Aquaculture Facility Open
Aquaculture is an important tool for solving growing worldwide food demand, but infectious diseases of the farmed animals represent a serious roadblock to continued industry growth. Therefore, it is essential to understand the microbial co…
View article: Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth
Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth Open
Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease and is often the precursor for more serious liver conditions such as nonalcoholic steatohepatitis and cirrhosis. Although the gut microbiome has been implica…
View article: Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts
Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts Open
The composition and structure of wood, which contains cellulose, hemicellulose, and lignin, prevent most organisms from using this common food source. Termites are a rare exception among animals, and they rely on a complex microbiota house…
View article: Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth
Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth Open
Background and Aims NAFLD is the most common form of liver disease and is often the precursor for more serious liver conditions such as NASH and cirrhosis. The gut microbiome has been implicated in the development of NAFLD, but studies hav…
View article: PmtA Regulates Pyocyanin Expression and Biofilm Formation in Pseudomonas aeruginosa
PmtA Regulates Pyocyanin Expression and Biofilm Formation in Pseudomonas aeruginosa Open
The opportunistic pathogen Pseudomonas aeruginosa expresses a small molecular weight, cysteine-rich protein (PmtA), identified as a metallothionein (MT) protein family member. The MT family proteins have been well-characterized in eukaryot…
View article: Draft Genome Sequence of Aeromonas popoffii ID682, Isolated from a Natural Water Source in Idaho
Draft Genome Sequence of Aeromonas popoffii ID682, Isolated from a Natural Water Source in Idaho Open
A draft genome sequence of Aeromonas popoffii ID682, isolated from a natural water source in Idaho, is presented here. A. popoffii is a relatively understudied species within a diverse, expanding freshwater genus of bacteria. Here, we desc…
View article: Draft Genome Sequence of Janthinobacterium lividum ID1246, Isolated from a Rainbow Trout Hatchery Biofilm
Draft Genome Sequence of Janthinobacterium lividum ID1246, Isolated from a Rainbow Trout Hatchery Biofilm Open
We present a draft genome sequence of Janthinobacterium lividum strain ID1246, isolated from within a rainbow trout hatchery raceway. Janthinobacterium spp. are well-known producers of antimicrobial compounds. Due to the unique isolation s…
View article: Detecting Flavobacterial Fish Pathogens in the Environment Using High-Throughput Community Analysis
Detecting Flavobacterial Fish Pathogens in the Environment Using High-Throughput Community Analysis Open
Diseases caused by the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum are major contributors of preventable losses in the aquaculture industry. The persistent and difficult to control infections caused by these ba…
View article: <i>Macrobdella decora</i> : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech
<i>Macrobdella decora</i> : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech Open
Building evidence implicates the gut microbiome in critical animal functions such as regulating digestion, nutrition, immune regulation, and development. Simplified, phylogenetically diverse models for hypotheses testing are necessary beca…
View article: High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon
High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon Open
Achieving strain-level resolution is a major obstacle for source tracking and temporal studies of microbiomes. In this study, we describe a novel deep-sequencing approach that provides species- and strain-level resolution of the neonatal m…
View article: Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes
Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes Open
Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental …
View article: Draft Genome Sequences of <i>Dysgonomonas</i> sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower Termite
Draft Genome Sequences of <i>Dysgonomonas</i> sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower Termite Open
Dysgonomonas spp. are facultative heterotrophs which colonize diverse environments, including the hindgut of the lower termite Reticulitermes flavipes . Dysgonomonas genomes are enriched for genes involving oligo- and polysaccharide utiliz…
View article: Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts
Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts Open
Different protist species which colonize the hindguts of wood feeding Reticulitermes termites are associated with endosymbiotic bacteria belonging to the genus Endomicrobium . In this study, we focused on the endosymbionts of three protist…
View article: Closed Genome Sequence of Aeromonas veronii Strain Hm21, an Isolate from the Medicinal Leech Hirudo verbana
Closed Genome Sequence of Aeromonas veronii Strain Hm21, an Isolate from the Medicinal Leech Hirudo verbana Open
Aeromonas veronii strain Hm21 was isolated from the medicinal leech and is used for genetic studies. We present here the 4.71-Mbp genome with a 56-kb plasmid and identify the mutations present in strains commonly used for genetic engineeri…
View article: Tracking Closely Related Enteric Bacteria at High Resolution in Fecal Samples of Premature Infants Using a Novel rRNA Amplicon
Tracking Closely Related Enteric Bacteria at High Resolution in Fecal Samples of Premature Infants Using a Novel rRNA Amplicon Open
Identifying and tracking microbial strains as microbiomes evolve is a major challenge in the field of microbiome research. Longitudinal microbiome samples of co-admitted twins from two different neonatal intensive care units (NICUs) were a…
View article: Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes
Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes Open
Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental …
View article: Effect of Gut Microbiota and <i>PNPLA3</i> rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth
Effect of Gut Microbiota and <i>PNPLA3</i> rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth Open
Context Nonalcoholic fatty liver disease (NAFLD) is the most common cause of liver disease, affecting approximately 3 in 10 obese children worldwide. Objective We aimed to investigate the potential relationship between gut microbiota and N…
View article: Gut Microbiota–Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice
Gut Microbiota–Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice Open
Rationale: The elderly experience profound systemic responses after stroke, which contribute to higher mortality and more severe long-term disability. Recent studies have revealed that stroke outcomes can be influenced by the composition o…
View article: Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas
Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas Open
Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of path…
View article: Effects of host species identity and diet on biodiversity of oral and rectal microbiomes of Puerto Rican bats
Effects of host species identity and diet on biodiversity of oral and rectal microbiomes of Puerto Rican bats Open
Microbiomes perform vital functions for their mammalian hosts, making them potential drivers of host evolution. Understanding effects of environmental factors and host characteristics on the composition and biodiversity of microbiomes may …