Lakhansing Pardeshi
LightNews LightNews
banner
lakhanp01.bsky.social
Lakhansing Pardeshi
@lakhanp01.bsky.social
26 followers 170 following 0 posts
PhD Candidate | Pangenomics, Bioinformatics, Pathogens | @w-u-r.bsky.social
Posts Replies Media Videos
Reposted by Lakhansing Pardeshi
sinamajidian.bsky.social
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Figure 1: (A) Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables compu- tation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade-based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Com- mon Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found us- ing the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method (sec- tion 2.6).
November 6, 2025 at 1:13 AM
Reposted by Lakhansing Pardeshi
audeber.bsky.social
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).

Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Labs in bacterial immunity
docs.google.com
November 4, 2025 at 3:06 PM
Reposted by Lakhansing Pardeshi
asantoslopez.bsky.social
Do plasmids really move around that much? Well, maybe not always

Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social

This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social

www.cell.com/cell-reports...
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
www.cell.com
October 22, 2025 at 5:47 PM
Reposted by Lakhansing Pardeshi
jsantoyo.bsky.social
Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
October 21, 2025 at 1:49 PM
Reposted by Lakhansing Pardeshi
who.int
Between 2018–2023, antibiotic resistance increased in over 40% of the pathogen–antibiotic combinations monitored, with an average annual rise of 5–15%.

Resistance is highest in the WHO South-East Asian & Eastern Mediterranean Regions, where 1 in 3 reported infections were resistant 👉 bit.ly/438Ta1u
Text reads “Antibiotic resistance is rising,” with an upward arrow and a “40%” warning icon. Below, a text box says: “Between 2018 and 2023, resistance increased in over 40% of the monitored pathogen–antibiotic combinations, with an annual rise of 5–15%.”
October 15, 2025 at 8:00 AM
Reposted by Lakhansing Pardeshi
misssalmonella.bsky.social
🧬 What if #plasmids weren’t competitors, but cooperators?
A new study in npj Antimicrobials & Resistance shows that many plasmids coexist within the same bacterium — and that non-resistant ones survive thanks to those carrying #AMR genes.
#AMR #Plasmids #OneHealth
🔗 doi.org/10.1038/s442...
Communities of plasmids as strategies for antimicrobial resistance gene survival in wastewater treatment plant effluent - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Communities of plasmids as strategies for antimicrobial resistance gene survival in wastewater treatment plant effluent
doi.org
October 15, 2025 at 6:14 PM
Reposted by Lakhansing Pardeshi
beatrizbeamud.bsky.social
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky

www.nature.com/articles/s41...
Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications
Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.
www.nature.com
October 8, 2025 at 8:59 AM
Reposted by Lakhansing Pardeshi
stcmicrobeblog.bsky.social
#MicroSky
surtlab.bsky.social Dave Baltrus 🦦 @surtlab.bsky.social · Oct 6
Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination

academic.oup.com/g3journal/ad...
Genomic correlates of tailocin sensitivity in Pseudomonas syringae
Abstract. Phage-derived bacteriocins, also referred to as tailocins, are structures encoded by bacterial genomes and deployed into the extracellular enviro
academic.oup.com
October 7, 2025 at 11:57 AM
Reposted by Lakhansing Pardeshi
curiouscoding.nl
Sassy is out now!

Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!

Available now wherever you get your code

With @rickbitloo.bsky.social

curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Sassy solves approximate string matching: finding all matches of a pattern in a text.
July 18, 2025 at 8:20 PM
Reposted by Lakhansing Pardeshi
phasegenomics.bsky.social
In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.
Phages with a broad host range are common across ecosystems - Nature Microbiology
Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.
www.nature.com
September 29, 2025 at 5:32 PM
Reposted by Lakhansing Pardeshi
craigmaclean.bsky.social
New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.

E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage

www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance genes and phage defense systems in E. coli
Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...
www.biorxiv.org
July 29, 2025 at 1:28 PM
Reposted by Lakhansing Pardeshi
zaminiqbal.bsky.social
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
September 25, 2025 at 9:29 PM
Reposted by Lakhansing Pardeshi
zaminiqbal.bsky.social
Super paper from the mighty Mia Winkler, @genomarit.bsky.social and Iren Lohr.
"We have previously shown that there were relatively few strain-sharing events across ecological niches...plasmid-sharing is considerably more common across niches than strain-sharing. "
www.biorxiv.org/content/10.1...
A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome
Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) ca...
www.biorxiv.org
September 17, 2025 at 10:12 PM
Reposted by Lakhansing Pardeshi
jsantoyo.bsky.social
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
September 18, 2025 at 11:15 AM
Reposted by Lakhansing Pardeshi
biorxiv-microbiol.bsky.social
Identification and Functional Insights into New Phage Tail-Like Bacteriocins (PTLBs) Targeting Pseudomonas aeruginosa as new antimicrobials https://www.biorxiv.org/content/10.1101/2025.08.20.671207v1
August 21, 2025 at 4:16 AM
Reposted by Lakhansing Pardeshi
jsantoyo.bsky.social
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @natcomms.nature.com
www.nature.com/articles/s41...
August 17, 2025 at 7:05 PM
Reposted by Lakhansing Pardeshi
bramvandijk.bsky.social
This is very cool. @sanmillan.bsky.social I wonder to what extend these non-random IS-dynamics are naturally selected for. Could it be the result of a long co-evolutionary history of ISs and bacteria? Are there differences in natural/non-natural antimicrobials?

www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation
Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...
www.biorxiv.org
August 18, 2025 at 8:15 AM
Reposted by Lakhansing Pardeshi
zaminiqbal.bsky.social
"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...
Protein structure alignment significance is often exaggerated
Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...
www.biorxiv.org
August 17, 2025 at 10:53 PM
Reposted by Lakhansing Pardeshi
jsantoyo.bsky.social
Mumemto: efficient maximal matching across pangenomes. #Pangenomes #VisualizationTool #PangenomeDiagnostic #Bioinformatics #Genomics #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
Mumemto: efficient maximal matching across pangenomes - Genome Biology
Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the…
genomebiology.biomedcentral.com
June 25, 2025 at 10:30 AM
Reposted by Lakhansing Pardeshi
jromeijn.bsky.social
The first paper of my PhD is now available as a preprint! 🎉

Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.
www.biorxiv.org
June 20, 2025 at 7:39 PM
Reposted by Lakhansing Pardeshi
ksbakes.bsky.social
Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n
www.biorxiv.org/content/10.1...
Defence systems drive accessory genome interactions in Pseudomonas aeruginosa
As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassin...
www.biorxiv.org
May 23, 2025 at 6:33 PM