Itzhak Mizrahi
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View article: Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function
Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function Open
Some microbes persist across diverse gut microbiomes, raising the question of what features define these core taxa and allow them to persist across hosts. Using the rumen microbiome as a model system, we show that core microbes exhibit dis…
View article: Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon
Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon Open
Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which reli…
View article: Mucinolysome in gut microbiomes of farm animals and humans
Mucinolysome in gut microbiomes of farm animals and humans Open
Mucins are glycoproteins that create a protective barrier protecting host tissues from microbial pathogens and are instrumental for host health. Here, we provide evidence that mucin glycan degradation in the gut can be mediated by mucinoly…
View article: Systematic discovery of bacterial symbionts in rumen ciliate protozoa
Systematic discovery of bacterial symbionts in rumen ciliate protozoa Open
Microbial interactions are fundamental to global ecological and evolutionary processes, exemplified by endosymbiosis between prokaryotes and single-cell eukaryotes that gave rise to organelles. While such associations remain widespread and…
View article: Editorial: thematic issue on interactions across microbial ecosystems
Editorial: thematic issue on interactions across microbial ecosystems Open
View article: Spatial constraints drive amylosome-mediated resistant starch degradation by <i>Ruminococcus bromii</i> in the human colon
Spatial constraints drive amylosome-mediated resistant starch degradation by <i>Ruminococcus bromii</i> in the human colon Open
Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which reli…
View article: Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance
Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance Open
The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of a…
View article: Understanding the Dynamics of Biomass Deconstruction b<i>y</i>the Cellulolytic Anaerobe<i>Clostridium thermocellum</i>
Understanding the Dynamics of Biomass Deconstruction b<i>y</i>the Cellulolytic Anaerobe<i>Clostridium thermocellum</i> Open
Clostridium thermocellum is one of the most efficient microorganisms for the deconstruction of cellulosic biomass. To achieve this high level of cellulolytic activity, C. thermocellum uses large multienzyme complexes known as cellulosomes …
View article: Unique Fn3‐like biosensor in <scp>σ<sup>I</sup></scp>/anti‐<scp>σ<sup>I</sup></scp> factors for regulatory expression of major cellulosomal scaffoldins in <i>Pseudobacteroides cellulosolvens</i>
Unique Fn3‐like biosensor in <span>σ<sup>I</sup></span>/anti‐<span>σ<sup>I</sup></span> factors for regulatory expression of major cellulosomal scaffoldins in <i>Pseudobacteroides cellulosolvens</i> Open
Lignocellulolytic clostridia employ multiple pairs of alternative σ/anti‐σ (SigI/RsgI) factors to regulate cellulosomal components for substrate‐specific degradation of cellulosic biomass. The current model has proposed that RsgIs use a se…
View article: Regional processes shape the structure of rumen microbial co‐occurrence networks
Regional processes shape the structure of rumen microbial co‐occurrence networks Open
Co‐occurrence networks offer insights into the complexity of microbial interactions, particularly in highly diverse environments where direct observation is challenging. However, identifying the scale at which local and non‐local processes…
View article: Three enzymes governed the rise of O2 on Earth
Three enzymes governed the rise of O2 on Earth Open
Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting…
View article: The radical impact of oxygen on prokaryotic evolution—enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third
The radical impact of oxygen on prokaryotic evolution—enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third Open
Molecular oxygen is a stable diradical. All O 2 ‐dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O 2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respirat…
View article: Phylogenomics and genetic analysis of solvent-producing Clostridium species
Phylogenomics and genetic analysis of solvent-producing Clostridium species Open
View article: Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases
Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases Open
Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid…
View article: A cellulosomal double‐dockerin module from <i>Clostridium thermocellum</i> shows distinct structural and cohesin‐binding features
A cellulosomal double‐dockerin module from <i>Clostridium thermocellum</i> shows distinct structural and cohesin‐binding features Open
Cellulosomes are intricate cellulose‐degrading multi‐enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohes…
View article: Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans
Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans Open
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the g…
View article: The underappreciated diversity of bile acid modifications
The underappreciated diversity of bile acid modifications Open
The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/M…
View article: Plasmid-encoded toxin defence mediates mutualistic microbial interactions
Plasmid-encoded toxin defence mediates mutualistic microbial interactions Open
View article: Scale-dependent signatures of microbial co-occurrence revealed via multilayer network analysis
Scale-dependent signatures of microbial co-occurrence revealed via multilayer network analysis Open
The composition of microbial communities underlies many ecosystem functions. Co-occurrence networks offer insights into the complexity of microbial interactions, particularly in highly diverse environments where direct observation is chall…
View article: Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases
Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases Open
Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3,467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmi…
View article: Affinity-induced covalent protein-protein ligation via the SpyCatcher-SpyTag interaction
Affinity-induced covalent protein-protein ligation via the SpyCatcher-SpyTag interaction Open
Production of economically viable bioethanol is potentially an environmentally and financially worthwhile endeavor. One major source for fermentable sugars is lignocellulose. However, lignocellulosic biomass is difficult to degrade, owing …
View article: Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission
Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission Open
Antimicrobial resistance (AMR) is a significant threat to public health. Plasmids are principal vectors of AMR genes, significantly contributing to their spread and mobility across hosts. Nevertheless, little is known about the dynamics of…
View article: Phylogenetic diversity of core rumen microbiota as described by cryo-ET
Phylogenetic diversity of core rumen microbiota as described by cryo-ET Open
Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture repr…
View article: The Underappreciated Diversity of Bile Acid Modifications
The Underappreciated Diversity of Bile Acid Modifications Open
View article: The origin and distribution of the main oxygen sensing mechanism across metazoans
The origin and distribution of the main oxygen sensing mechanism across metazoans Open
Oxygen sensing mechanisms are essential for metazoans, their origin and evolution in the context of oxygen in Earth history are of interest. To trace the evolution of a main oxygen sensing mechanism among metazoans, the hypoxia induced fac…
View article: Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery Open
The archaeal Asgard superphylum currently stands as the most promising prokaryotic candidate, from which eukaryotic cells emerged. This unique superphylum encodes for eukaryotic signature proteins (ESP) that could shed light on the origin …
View article: A link between genotype and cellular architecture in microbiome members as revealed by cryo-EM
A link between genotype and cellular architecture in microbiome members as revealed by cryo-EM Open
Microbial taxonomy is not yet sufficient to describe microbe functionality and ecology. Since function is often linked to structure, we sought here to use cryo-electron microscopy and tomography to analyze microbial cellular architecture a…
View article: Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits
Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits Open
The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed effic…
View article: Mapping the deformability of natural and designed cellulosomes in solution
Mapping the deformability of natural and designed cellulosomes in solution Open
View article: Nanoscale resolution of microbial fiber degradation in action
Nanoscale resolution of microbial fiber degradation in action Open
The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation…