Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor DOI Creative Commons
Miaoxiao Wang, Xiaoli Chen, Xiaonan Liu

et al.

Cell Reports, Journal Year: 2022, Volume and Issue: 40(13), P. 111410 - 111410

Published: Sept. 1, 2022

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within linear pathway, phenomenon termed division of labor (MDOL). However, little is known about how such behaviors shape microbial communities. Here, we derive theoretical framework define the assembly community that degrades an organic compound through MDOL. The indicates ensure stability, performing initial should hold growth advantage (m) over "private benefit" (n) strain last step. steady-state frequency then determined by quotient n and m. Our experiments show accurately predicts our synthetic consortia degrade naphthalene results provide insights for designing managing stable systems pathway optimization.

Language: Английский

CRISPR/Cas-Based Genome Editing for Human Gut Commensal Bacteroides Species DOI

Linggang Zheng,

Yang Tan, Yucan Hu

et al.

ACS Synthetic Biology, Journal Year: 2022, Volume and Issue: 11(1), P. 464 - 472

Published: Jan. 6, 2022

Bacteroides is the most abundant genus in human gut microbiome and has been increasingly used as model organisms for studying function ecology of microbiome. However, genome editing tools such commensal microbes are still lacking. Here we developed a versatile, highly efficient CRISPR/Cas-based tool that allows markerless gene deletion insertion species. We constructed multiple CRISPR/Cas systems all-in-one Bacteroides–E. coli shuttle plasmids systematically evaluated efficiency thetaiotaomicron, including mode Cas protein expression (constitutive, inducible), different proteins (FnCas12a, SpRY, SpCas9), sgRNAs. Using anhydrotetracycline (aTc)-inducible CRISPR/FnCas12a system, successfully deleted large genomic fragments up to 50 kb study metabolic clusters. Furthermore, demonstrated can be broadly applied engineer species, fragilis, ovatus, uniformis, vulgatus. envision will greatly facilitate mechanistic studies development engineered live biotherapeutics.

Language: Английский

Citations

49
Division of labor for substrate utilization in natural and synthetic microbial communities DOI Creative Commons
Razieh Rafieenia, Eliza Atkinson, Rodrigo Ledesma‐Amaro

et al.

Current Opinion in Biotechnology, Journal Year: 2022, Volume and Issue: 75, P. 102706 - 102706

Published: March 4, 2022

In natural ecosystems, microorganisms live in communities where each member interacts with the others and environment to efficiently utilise available resources. Division of Labor (DOL) is an evolutionary strategy that evolved by microbial accomplish complex tasks. Current bio-based technologies could also benefit from DOL construct robust cell factories expanded metabolic capabilities. Here, we review some remarkable examples how used consortia utilize a range substrates. Also, most recent studies towards engineering design synthetic for efficient substrate utilization bioproduction.

Language: Английский

Citations

47
dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes DOI Creative Commons
Jinfang Zheng,

Boyang Hu,

Xinpeng Zhang

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D557 - D563

Published: Nov. 18, 2022

Abstract Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing assembly have produced numerous metagenome assembled genomes (MAGs). We updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) include the following new data features: (i) ∼498 000 CAZymes ∼169 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, marine) environments; (ii) Glycan substrates 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search eCAMI subfamily majority voting) (the agreed on 4183 substrate assignments); (iii) A redesigned CGC page graphical display compositions, alignment query subject PUL (polysaccharide utilization loci) dbCAN-PUL, table support predicted substrates; (iv) statistics organize all easy access according taxonomic phyla; (v) batch download page. In summary, this highlights glycan microbiomes. Future work will implement prediction function dbCAN2 web server.

Language: Английский

Citations

45
Potential effects of nectar microbes on pollinator health DOI
Valerie N. Martin, Robert N. Schaeffer, Tadashi Fukami

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1853)

Published: May 2, 2022

Floral nectar is prone to colonization by nectar-adapted yeasts and bacteria via air-, rain-, animal-mediated dispersal. Upon colonization, microbes can modify chemical constituents that are plant-provisioned or impart their own through secretion of metabolic by-products antibiotics into the environment. Such modifications have consequences for pollinator perception quality, as microbial metabolism leave a distinct imprint on olfactory gustatory cues inform foraging decisions. Furthermore, direct interactions between pollinators microbes, well consumption modified nectar, potential affect health both positively negatively. Here, we discuss integrate recent findings from research plant–microbe–pollinator health. We then explore future avenues could shed light myriad ways in which health, including taxonomic diversity vertebrate invertebrate rely this reward. This article part theme issue ‘Natural processes influencing health: chemistry landscapes’.

Language: Английский

Citations

42
Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor DOI Creative Commons
Miaoxiao Wang, Xiaoli Chen, Xiaonan Liu

et al.

Cell Reports, Journal Year: 2022, Volume and Issue: 40(13), P. 111410 - 111410

Published: Sept. 1, 2022

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within linear pathway, phenomenon termed division of labor (MDOL). However, little is known about how such behaviors shape microbial communities. Here, we derive theoretical framework define the assembly community that degrades an organic compound through MDOL. The indicates ensure stability, performing initial should hold growth advantage (m) over "private benefit" (n) strain last step. steady-state frequency then determined by quotient n and m. Our experiments show accurately predicts our synthetic consortia degrade naphthalene results provide insights for designing managing stable systems pathway optimization.

Language: Английский

Citations

42