Piyush Ranjan

University of Michigan | U-M · Division of Pulmonary and Critical Care Medicine

Bacterial detection and identification methods can be broadly classified as either untargeted with expansive taxonomic coverage or targeted with narrow taxonomic focus. Untargeted approaches, such as culture and sequencing, are often time-consuming and/or costly, whereas targeted methods, such as PCR, can offer faster and more cost-effective result...

Although the lungs were once considered a sterile environment, advances in sequencing technology have revealed dynamic, low-biomass communities in the respiratory tract, even in health. Key features of these communities-composition, diversity, and burden-are consistently altered in lung disease, associate with host physiology and immunity, and can...

Rationale: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown. Objectives: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis. Methods: We analyzed 16S rRNA gene and shotgun...

Pulmonary fibrosis is a chronic and often fatal disease. The pathogenesis is characterized by aberrant repair of lung parenchyma resulting in loss of physiological homeostasis, respiratory failure and death. The immune response in pulmonary fibrosis is dysregulated. The gut microbiome is a key regulator of immunity. The role of the gut microbiome i...

Red blood cells (RBCs), traditionally recognized for their role in transporting oxygen, play a pivotal role in the body's immune response by expressing TLR9 and scavenging excess host cell-free DNA. DNA capture by RBCs leads to accelerated RBC clearance and triggers inflammation. Whether RBCs can also acquire microbial DNA during infections is unkn...

ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively sequence reads of target species in real-time. This enables efficient microbial enrichment for applications such as microbial abundance estimation and is particularly beneficial for metagenomic samples with a very high fraction of non-target reads (> 99% can be human rea...

Here we introduce SNIKT, a command-line tool for sequence-independent visual confirmation and input-assisted removal of adapter contamination in whole-genome shotgun or metagenomic shotgun long-read sequencing DNA or RNA data. Availability and Implementation SNIKT is implemented in R and is compatible with Unix-like platforms. The source code, alo...

Metagenomics holds potential to improve clinical diagnostics of infectious diseases, but DNA from clinical specimens is often dominated by host-derived sequences. To address this, researchers employ host-depletion methods. Laboratory-based host-depletion methods, however, are costly in terms of time and effort, while computational host-depletion me...

We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 s of sequencing data, the classifier achieves significantly higher accuracy than base calling follow...

Gas hydrates harbor gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences gener...

We report an improved, nearly closed, high-quality draft genome reconstruction of the Candida albicans CHN1 strain (ATCC MYA-4779), a human isolate, using Illumina and Nanopore sequencing. Covering six complete and two partial nuclear chromosomes along with a partial mitochondrial genome, this assembly is 14,787,852 bases in size, with 5,935 genes.

Single-molecule sequencers made by Oxford Nanopore provide results in real time as DNA passes through a nanopore and can eject a molecule after it has been partly sequenced. However, the computational challenge of deciding whether to keep or reject a molecule in real time has limited the application of this capability. We present SquiggleNet, the f...

[This corrects the article DOI: 10.3389/fmicb.2015.00998.].

The Centers for Disease Control and Prevention estimates that VRE causes an estimated 54,000 infections and 539 million dollars in attributable health care costs annually. Despite improvements in hand washing, environmental cleaning, and antibiotic use, VRE is still prevalent in many hospitals. There is a pressing need to better understand the proc...

Gas hydrates harbor gigatons of natural gas, yet their microbiomes remain mysterious. We bioprospected methane hydrate-bearing sediments from under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244) using 16S rRNA gene amplicon, metagenomic, and metaproteomic analysis. Atribacteria (JS-1 Genus 1) sequences rose in abundance with increasing sedimen...

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SA...

Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautile...

Maps showing the vent fields ABE and Tu'i Malila at the Eastern Lau Spreading Center where individual snails used in the experimental treatments were collected.

List of differentially expressed SEED Level 1 subsystems including normalized transcript abundance and false discovery rate (FDR) values.

Normalized abundance of transcripts in all 12 metatranscriptomes corresponding to SEED subsystem functional proteins annotated in MEGAN5.

List of differentially expressed SEED Level functional proteins as annotated in MEGAN5 including normalized transcript abundance and false discovery rate (FDR) values.

Abundance of specific transcripts of interest (see Materials and Methods) in all 12 metatranscriptomes from manual searches of processed BLASTX results (bit score >50) normalized to 100 000 non-rRNA reads per metatranscriptome.

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins...

CRISPR/Cas9 systems are a versatile tool for genome editing due to the highly efficient targeting of DNA sequences complementary to their RNA guide strands. However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. A better understanding of the CRISPR/Cas9 specificity is needed...

A top–down predictor, called TpPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1 st layer of the prediction engine is for identifying a query protein as transport protein or not; the 2 nd layer for the main functional class; and the 3 rd layer for the s...

Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closely related to the biological function of an uncharacterized pro-tein. Particularly, with the avalanche of protein sequences generated...

Noncompetitive inhibitors of sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) orthologue (PfATP6) of P. falciparum have important therapeutic value in the treatment of malaria. Artemisinin and its analogues are one such class of inhibitors which bind to a hydrophobic pocket located in the transmembrane region of PfATP6 near the biomembrane surface a...