Ruiwen Hu, PhD (@MicrobeCookie) header
Ruiwen Hu, PhD (@MicrobeCookie) profile picture

Ruiwen Hu, PhD

@MicrobeCookie

LBNL Postdoc Researcher; Environmental microbiologist

 Berkeley, CA
Joined November 2022
  • Tweets763
  • Following287
  • Followers151
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Photo by Ruiwen Hu, PhD (@MicrobeCookie)Photo by Ruiwen Hu, PhD (@MicrobeCookie)
Ruiwen Hu, PhD retweeted
Frederik Schulz (@frederikschu) profile picture
Frederik Schulz
@frederikschu4h
New paper from our lab led by @mikebartgeier : A global survey of >30,000 assembled metagenomes reveals vast unexplored protist diversity. Recovered sequences suggest the existence of at least 13 deeply divergent lineages and provide a resource to guide their cultivation and characterization. nature.com/articles/s41467-0…

Global environmental genomics reveals vast uncultivated protist diversity and taxonomic blind spots

Nature Communications - In this study, the authors analyze over 30,000 assembled metagenomes across ecosystems to uncover hidden protist diversity, including major novel uncultivated lineages, and...

nature.com
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Ruiwen Hu, PhD retweeted
Yongyu Zhang (@yongyu_zhang) profile picture
Yongyu Zhang@yongyu_zhangSep 29
Escalating Herbicide Loads as Underappreciated Global Disruptors of Marine Phytoplankton and Biogeochemical Cycles pubs.acs.org/esthag/article-…
Escalating Herbicide Loads as Underappreciated Global Disruptors of Marine Phytoplankton and...

Escalating Herbicide Loads as Underappreciated Global Disruptors of Marine Phytoplankton and...

Abstract. Under accelerating climate change and anthropogenic pressures, the global oceans face unprecedented threats from land-to-ocean contaminant discha

pubs.acs.org
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Ruiwen Hu, PhD retweeted
Vivek Mutalik (@vivek_mutalik) profile picture
Vivek Mutalik@vivek_mutalikSep 29
annualreviews.org/content/jo… Scaling Phage-Bacteria Interaction Contexts: From Pairwise Mechanisms to Community Dynamics

Scaling Phage-Bacteria Interaction Contexts: From Pairwise Mechanisms to Community Dynamics

Bacteriophages (phages), viruses that parasitize bacteria, hold tremendous potential as antimicrobial agents, microbiome modulators, and industrial biocontrol tools; yet clinical and environmental...

annualreviews.org
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Ruiwen Hu, PhD retweeted
Yongyu Zhang (@yongyu_zhang) profile picture
Yongyu Zhang@yongyu_zhangSep 24
I am pleased to share our paper just published in Science Advances, titled "Global dispersal of macroalgae-derived recalcitrant DOC may substantially contribute to deep-ocean carbon storage". science.org/doi/10.1126/scia…
Global dispersal of macroalgae-derived recalcitrant DOC may substantially contribute to deep-ocean...

Global dispersal of macroalgae-derived recalcitrant DOC may substantially contribute to deep-ocean...

Macroalgae, the dominant primary producers of Earth’s most productive coastal vegetated ecosystems and a vital component driving ocean carbon sequestration, produce ∼5 to 80% of their net primary...

science.org
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Ruiwen Hu, PhD retweeted
Frederik Schulz (@frederikschu) profile picture
Frederik Schulz
@frederikschuSep 22
New study supported by our lab published in Cell: Incendiamoeba cascadensis, a newly described geothermal amoeba, divides at 63°C, setting a new upper temperature record for eukaryotic life. Comparative genomics and cell-biological analyses reveal adaptations linked to protein homeostasis, genome stability, and environmental sensing. sciencedirect.com/science/ar…
Image from Frederik Schulz (@frederikschu)
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Ruiwen Hu, PhD retweeted
Vivek Mutalik (@vivek_mutalik) profile picture
Vivek Mutalik@vivek_mutalikSep 19
Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them....Our new preprint takes this on 🧵👇
Image from Vivek Mutalik (@vivek_mutalik)
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Ruiwen Hu, PhD retweeted
Frederik Schulz (@frederikschu) profile picture
Frederik Schulz
@frederikschuSep 10
Metagenomes from 150 permafrost samples show that microbial diversity drops with depth, but only in the active layer as degradation progresses. Pithoviridae, Caulimoviridae, and virulence genes for adhesion, biofilm formation, and immune regulation were enriched in the frozen fringe, the thin transition between active and frozen ground. Giant virus-associated virophages rose as permafrost degraded. doi.org/10.1038/s41467-026-7…
Hydrothermal regimes regulate microbiome patterns across vertical profile and their responses to...

Hydrothermal regimes regulate microbiome patterns across vertical profile and their responses to...

Nature Communications - Here, the authors surveyed the vertical microbiome in the Qinghai-Tibet Plateau and assessed the degradation patterns, biogeochemical cycling, and nutrient loss across these...

nature.com
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EBI Director John Coates joined global leaders at WCMS 2026 to explore marine innovation, scalable bioprocesses, and macroalgae’s potential to advance the global bioeconomy. The future of marine innovation starts with collaboration! #WCMS2026 #Bioeconomy #OceanInnovation
Image from Energy & Biosciences Institute (@EnergyBioscien1)
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Ruiwen Hu, PhD retweeted
Yongyu Zhang (@yongyu_zhang) profile picture
Yongyu Zhang@yongyu_zhangSep 1
What if “old” ocean carbon doesn’t have to be old? Our new study shows that sustained algal–bacterial interactions can rapidly transform algal-derived carbon into recalcitrant particulate carbon, with a radiocarbon age offset of >400 years in just 2 years nature.com/articles/s41467-0…
Image from Yongyu Zhang (@yongyu_zhang)
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Ruiwen Hu, PhD retweeted
Frederik Schulz (@frederikschu) profile picture
Frederik Schulz
@frederikschuAug 31
New study from our lab, out now in Nature Biotechnology: Genome-resolved metagenomics and single-cell genomics have yielded millions of microbial genomes. Could a large fraction of these uncultivated bacteria and archaea be symbionts? We identified genomic signatures of host dependence across global metagenomic data, suggesting that 15–23% may live in symbiosis. The resulting SymGs catalog and our symclatron software provide new resources for studying and engineering host–microbe interactions. nature.com/articles/s41587-0…
A genomic catalog of Earth’s bacterial and archaeal symbionts

A genomic catalog of Earth’s bacterial and archaeal symbionts

Nature Biotechnology - Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

nature.com
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A first-of-its-kind use of a #methanogen for leucine production! The organism in question: Methanothermobacter marburgensis. #biotechnology #methane #archaea #MetabolicEngineering @TrendsinBiotech sciencedirect.com/science/ar…
Image from Evgenii Protasov (@protasov_evgeni)
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Ruiwen Hu, PhD retweeted
Jianjun Wang (@jianjunwang) profile picture
Jianjun Wang@jianjunwangAug 16
How does warming alter marine dissolved organic matter? A global study tracks "DOM thermal responses" - shifts in molecular composition linked to temperature. Discover how these thermal responses and photochemistry shape the future ocean carbon sink. biorxiv.org/content/10.1101/…
Image from Jianjun Wang (@jianjunwang)
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Ruiwen Hu, PhD retweeted
Vivek Mutalik (@vivek_mutalik) profile picture
Vivek Mutalik@vivek_mutalikAug 14
This framework turns weeks of lab screening into ML predictions that can guide treatment decisions with additional validation. This work & our recent P. aeruginosa study, builds the data foundations necessary for genome-guided phage therapy. Preprint: biorxiv.org/content/10.64898…
A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to...

A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to...

Klebsiella pneumoniae is a WHO critical-priority pathogen for which strain-specific bacteriophages are being explored as precision antimicrobials, yet rapid phage-host matching remains a major...

biorxiv.org
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Ruiwen Hu, PhD retweeted
Frederik Schulz (@frederikschu) profile picture
Frederik Schulz
@frederikschuAug 13
New study from our lab: GVMAGs V2, a comprehensive curated genome resource and taxonomic framework for over 18k giant viruses, including representatives of 712 novel genera, 13 novel families, and a proposed new order. Nearly 70% of orthogroups representing 2.5 million giant virus proteins remain uncharacterized - a treasure trove for biotechnological applications. Read the paper in Nature Microbiology: doi.org/10.1038/s41564-026-0…
Genomic catalogue of giant viruses reveals expanded diversity and functional potential

Genomic catalogue of giant viruses reveals expanded diversity and functional potential

Nature Microbiology - This curated genome-resolved, metagenomic resource expands the known diversity of Nucleocytoviricota and Mirusviricota lineages.

nature.com
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Ruiwen Hu, PhD retweeted
A. Murat Eren (Meren) (@merenbey) profile picture
A. Murat Eren (Meren)@merenbeyAug 12
If you heard about #anvio but never had a chance to figure out what it really is, please consider watching this 12-minute video by Iva Veseli: youtube.com/watch?v=fExu_euH… It is a short and sweet introduction to what (and what not) to expect from anvi'o 😇
A brief introduction to the anvi'o software platform for microbial 'omics research

A brief introduction to the anvi'o software platform for microbial 'omics research

Anvi'o is a free, open-source, community-driven software for analys...

youtube.com
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Ruiwen Hu, PhD retweeted
Vivek Mutalik (@vivek_mutalik) profile picture
Vivek Mutalik@vivek_mutalikJul 25
Lead by Edwin Rivera-Lopez & @LucasMoriniere With @microdudley @PSUmBiome @LBNLBioSci @AdamArkinLab Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7 biorxiv.org/content/10.64898…
Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic...

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic...

The outermost surface layers of Gram-negative bacteria determine phage access to terminal receptors, yet their genetic basis has been mapped almost exclusively in laboratory strains that lack them....

biorxiv.org
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Evolving strategies for #virus discovery #microbiology #virology #viruses @MicrobioSoc doi.org/10.1099/mgen.0.00178…
Image from Evgenii Protasov (@protasov_evgeni)
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Ruiwen Hu, PhD retweeted
Cell Reports (@CellReports) profile picture
Cell Reports@CellReportsJul 10
Synthetic ecology of coastal ecosystems dlvr.it/TTRxwk
Synthetic ecology of coastal ecosystems

Synthetic ecology of coastal ecosystems

Qian et al. review how multitrophic interactions shape coastal ecosystem functions and identify interaction principles and functional modules for synthetic community (SynCom) design. They propose a...

cell.com
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Ruiwen Hu, PhD retweeted
Xiyang Dong (@xiyang_dong) profile picture
Xiyang Dong@xiyang_dongJul 8
Pathogen context reshapes antimicrobial peptide generation biorxiv.org/content/10.64898…
Pathogen context reshapes antimicrobial peptide generation

Pathogen context reshapes antimicrobial peptide generation

Antimicrobial peptides are a promising source of new anti-infective agents, but their discovery is limited by a practical bottleneck: selecting a small set of candidates to synthesize and test for a...

biorxiv.org
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Ruiwen Hu, PhD retweeted
Tominaga K. (tomiken) (@pacyc1841) profile picture
Tominaga K. (tomiken)@pacyc1841Jun 19
The biology of jumbo phages | Nature Communications nature.com/articles/s41467-0…
The biology of jumbo phages

The biology of jumbo phages

Nature Communications - Jumbo phages are bacterial viruses with double-stranded DNA genomes exceeding 200 kb. In this Review, Sam van Beljouw & Li Yuping examine the biology of these...

nature.com
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