Shunsuke Adachi, Matt Stata, Duncan G Martin, Shifeng Cheng, Hongbing Liu, Xin-Guang Zhu, Rowan F Sage

Plant Physiol 2023 Jan 2;191(1):233-251. doi: 10.1093/plphys/kiac467.

PMID: 36200882

Abstract

Flaveria is a leading model for C4 plant evolution due to the presence of a dozen C3-C4 intermediate species, many of which are associated with a phylogenetic complex centered around Flaveria linearis. To investigate C4 evolution in Flaveria, we updated the Flaveria phylogeny and evaluated gas exchange, starch δ13C, and activity of C4 cycle enzymes in 19 Flaveria species and 28 populations within the F. linearis complex. A principal component analysis identified six functional clusters: (1) C3, (2) sub-C2, (3) full C2, (4) enriched C2, (5) sub-C4, and (6) fully C4 species. The sub-C2 species lacked a functional C4 cycle, while a gradient was present in the C2 clusters from little to modest C4 cycle activity as indicated by δ13C and enzyme activities. Three Yucatan populations of F. linearis had photosynthetic CO2 compensation points equivalent to C4 plants but showed little evidence for an enhanced C4 cycle, indicating they have an optimized C2 pathway that recaptures all photorespired CO2 in the bundle sheath (BS) tissue. All C2 species had enhanced aspartate aminotransferase activity relative to C3 species and most had enhanced alanine aminotransferase activity. These aminotransferases form aspartate and alanine from glutamate and in doing so could help return photorespiratory nitrogen (N) from BS to mesophyll cells, preventing glutamate feedback onto photorespiratory N assimilation. Their use requires upregulation of parts of the C4 metabolic cycle to generate carbon skeletons to sustain N return to the mesophyll, and thus could facilitate the evolution of the full C4 photosynthetic pathway.

Pierre H. H. Schneeberger, Chen Yang Kevin Zhang, Jessica Santilli, Bo Chen, Wei Xu, Youngho Lee, Zonelle Wijesinha Elaine Reguera-Nuñez, Noelle Yee, Musawir Ahmed, Kristen Boonstra, Rayoun Ramendra, Courtney W. Frankel, Scott M. Palmer  Jamie L. Todd , Tereza Martinu, Bryan Coburn

Am J Respir Crit Care Med 2022 Dec 15;206(12):1495-1507. doi: 10.1164/rccm.202110-2413OC.

PMID: 35876129

Abstract

Rationale: It remains unclear how gastroesophageal reflux disease (GERD) affects allograft microbial community composition in lung transplant recipients and its impact on lung allograft inflammation and function.

Objectives: Our objective was to compare the allograft microbiota in lung transplant recipients with or without clinically diagnosed GERD in the first year after transplant and assess associations between GERD, allograft microbiota, inflammation, and acute and chronic lung allograft dysfunction (ALAD and CLAD).

Methods: A total of 268 BAL samples were collected from 75 lung transplant recipients at a single transplant center every 3 months after transplant for 1 year. Ten transplant recipients from a separate transplant center provided samples before and after antireflux Nissen fundoplication surgery. Microbial community composition and density were measured using 16S ribosomal RNA gene sequencing and quantitative polymerase chain reaction, respectively, and inflammatory markers and bile acids were quantified.

Measurements and Main Results: We observed a range of allograft community composition with three discernible types (labeled community state types [CSTs] 1-3). Transplant recipients with GERD were more likely to have CST1, characterized by high bacterial density and relative abundance of the oropharyngeal colonizing genera Prevotella and Veillonella. GERD was associated with more frequent transitions to CST1. CST1 was associated with lower inflammatory cytokine concentrations than pathogen-dominated CST3 across the range of microbial densities observed. Cox proportional hazard models revealed associations between CST3 and the development of ALAD/CLAD. Nissen fundoplication decreased bacterial load and proinflammatory cytokines.

Conclusions: GERD was associated with a high bacterial density, Prevotella- and Veillonella-dominated CST1. CST3, but not CST1 or GERD, was associated with inflammation and early development of ALAD and CLAD. Nissen fundoplication was associated with a reduction in microbial density in BAL fluid samples, especially the CST1-specific genus, Prevotella.

Yasaman Ghorbani BSc, Katherine J. P. Schwenger PhD, Divya Sharma PhD, Hyejung Jung MSc, Jitender Yadav PhD, Wei Xu PhD, Wendy Lou PhD, Susan Poutanen MD, Susy S. Hota MD, Elena M. Comelli

Diabetes Obes Metab 2023 Feb;25(2):479-490. doi: 10.1111/dom.14891.

PMID: 36239189

Abstract

Aim: To assess the effects of faecal microbial transplant (FMT) from lean people to subjects with obesity via colonoscopy.

Material and methods: In a double-blind, randomized controlled trial, subjects with a body mass index ≥ 35 kg/m² and insulin resistance were randomized, in a 1:1 ratio in blocks of four, to either allogenic (from healthy lean donor; n = 15) or autologous FMT (their own stool; n = 13) delivered in the caecum and were followed for 3 months. The main outcome was homeostatic model assessment of insulin resistance (HOMA-IR) and secondary outcomes were glycated haemoglobin levels, lipid profile, weight, gut hormones, endotoxin, appetite measures, intestinal microbiome (IM), metagenome, serum/faecal metabolites, quality of life, anxiety and depression scores.

Results: In the allogenic versus autologous groups, HOMA-IR and clinical variables did not change significantly, but IM and metabolites changed favourably (P < 0.05): at 1 month, Coprococcus, Bifidobacterium, Bacteroides and Roseburia increased, and Streptococcus decreased; at 3 months, Bacteroides and Blautia increased. Several species also changed significantly. For metabolites, at 1 month, serum kynurenine decreased and faecal indole acetic acid and butenylcarnitine increased, while at 3 months, serum isoleucine, leucine, decenoylcarnitine and faecal phenylacetic acid decreased. Metagenomic pathway representations and network analyses assessing relationships with clinical variables, metabolites and IM were significantly enhanced in the allogenic versus autologous groups. LDL and appetite measures improved in the allogenic (P < 0.05) but not in the autologous group.

Conclusions: Overall, in those with obeisty, allogenic FMT via colonoscopy induced favourable changes in IM, metabolites, pathway representations and networks even though other metabolic variables did not change. LDL and appetite variables may also benefit.

Michael Kanaris, Jimmy Poulin, Dea Shahinas, Daniel Johnson, Valerie M. Crowley, Geoffrey Fucile, Nicholas Provart, Dinesh Christendat

Plant J 2022 Feb;109(4):789-803. doi: 10.1111/tpj.15590.

PMID: 34797933

Abstract

The shikimate pathway plays a central role in the biosynthesis of aromatic amino acids and specialized metabolites in plants. The first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) serves as a key regulatory point for the pathway in various organisms. These enzymes are important in regulating the shikimate pathway in multiple microbial systems. The mechanism of regulation of DAHPS is poorly understood in plants, and the role of tyrosine (Tyr) with respect to the three DAHPS isozymes from Arabidopsis thaliana was investigated. In vitro enzymatic analyses established that Tyr does not function as an allosteric regulator for the A. thaliana DAHPS isozymes. In contrast, Arabidopsis T-DNA insertional mutants for the DAHPS1 locus, dahps1, are hypersensitive to elevated Tyr. Tyr hypersensitivity can be reversed with tryptophan and phenylalanine supplementation, indicating that Tyr is affecting the shikimate pathway flux in the dahps1 mutant. Tyr treatment of Arabidopsis seedlings showed reduced accumulation of overexpressed DAHPS2 in the chloroplast. Further, bimolecular fluorescence complementation studies revealed that DAHPS2 interacts with a 14-3-3 protein in the cytosol, and this interaction is enhanced with Tyr treatment. This interaction with 14-3-3 may retain DAHPS2 in the cytosol, which prevents its ability to function in the chloroplast with elevated Tyr.

Cameron P. So, Mia M. Sibolibane, Arthur E. Weis

Am J Bot 2022 Nov;109(11):1893-1905. doi: 10.1002/ajb2.16083.

PMID: 36219500

Abstract

Premise: The evolutionary response of a trait to environmental change depends upon the level of additive genetic variance. It has been long argued that sustained selection will tend to deplete additive genetic variance as favored alleles approach fixation. Non-additive genetic variance, due to interactions among alleles within and between loci, does not immediately contribute to an evolutionary response. However, shifts in the allele frequencies within and between interacting loci may convert non-additive variance into additive variance. Here we consider the possibility that an environmental shift may alter allelic interactions in ways that convert dominance into additive genetic variance.

Methods: We grew a pedigreed population of Brassica rapa in greenhouse and field conditions. The field conditions mimicked agricultural conditions from which the base population was drawn, while the greenhouse featured benign conditions. We used Bayesian models to estimate the additive, dominance, and maternal components of quantitative genetic variance. We also estimated genetic correlations across environments using parental breeding values.

Results: Although the additive genetic variance was elevated in the greenhouse condition, no consistent pattens emerged that would indicate a conversion of dominance variance. The unusually low genetic variance and broad confidence intervals for the variance estimates obtained through this analysis preclude definitive interpretations.

Conclusions: Further studies are needed to determine whether between-environment changes in additive genetic variance can be traced to conversion of dominance variance.

Saranya Sivaraj, Julia K Copeland, Anshu Malik, Elisa Pasini, Marc Angeli, Amirhossein Azhie, Shahid Husain, Deepali Kumar, Johane Allard, David S Guttman, Atul Humar, Mamatha Bhat

Clin Transplant 2022 Feb;36(2):e14534. doi: 10.1111/ctr.14534

PMID: 34781411

Abstract

Long-term survival after Liver Transplantation (LT) is often compromised by infectious and metabolic complications. We aimed to delineate alterations in intestinal microbiome (IM) over time that could contribute to medical complications compromising long-term survival following LT. Fecal samples from LT recipients were collected at 3 months (3 M) and 6 months (6 M) post-LT. The bacterial DNA was extracted using E.Z.N.A. Stool DNA Kit and 16S rRNA gene sequencing at V4 hypervariable region was performed. DADA2 and Phyloseq was implemented to analyze the taxonomic composition. Differentially abundant taxa were identified by metagenomeSeq and LEfSe. Piphillin, an Inferred functional metagenomic analysis tool was used to study the bacterial functional content. For comparison, healthy samples were extracted from NCBI and analyzed similarly. The taxonomic & functional profiles of LT recipients were validated with metagenomic sequencing data from animals exposed to immunosuppressants using Venny. Our findings provide a new perspective on longitudinal increase in specific IM communities post-LT along with an increase in bacterial genes associated with metabolic and infectious disease.

Reneé Robinson, Vishwanath Sollapura, Philippe Couroux, Dave Sprott, Michael Ravensdale, Elizabeth Routly, Tim Xing, Laurian S. Robert

Plant J 2021 Sep;107(5):1546-1568. doi: 10.1111/tpj.15219

PMID: 33650121

Abstract

Successful pollination in Brassica brings together the mature pollen grain and stigma papilla, initiating an intricate series of molecular processes meant to eventually enable sperm cell delivery for fertilization and reproduction. At maturity, the pollen and stigma cells have acquired proteomes, comprising the primary molecular effectors required upon their meeting. Knowledge of the roles and global composition of these proteomes in Brassica species is largely lacking. To address this gap, gel-free shotgun proteomics was performed on the mature pollen and stigma of Brassica carinata, a representative of the Brassica family and its many crop species (e.g. Brassica napus, Brassica oleracea and Brassica rapa) that holds considerable potential as a bio-industrial crop. A total of 5608 and 7703 B. carinata mature pollen and stigma proteins were identified, respectively. The pollen and stigma proteomes were found to reflect not only their many common functional and developmental objectives, but also the important differences underlying their cellular specialization. Isobaric tag for relative and absolute quantification (iTRAQ) was exploited in the first analysis of a developing Brassicaceae stigma, and revealed 251 B. carinata proteins that were differentially abundant during stigma maturation, providing insight into proteins involved in the initial phases of pollination. Corresponding pollen and stigma transcriptomes were also generated, highlighting functional divergences between the proteome and transcriptome during different stages of pollen-stigma interaction. This study illustrates the investigative potential of combining the most comprehensive Brassicaceae pollen and stigma proteomes to date with iTRAQ and transcriptome data to provide a unique global perspective of pollen and stigma development and interaction.

Lauren LeMay-Nedjelski, Chloe Yonemitsu, Michelle R Asbury, James Butcher, Sylvia H Ley, Anthony J Hanley, Alex Kiss, Sharon Unger, Julia K Copeland, Pauline W Wang, Alain Stintzi, Lars Bode, and Deborah L O’Connor

J Nutr 2021 Nov 2;151(11):3431-3441. doi: 10.1093/jn/nxab270.

PMID: 34510198

Abstract

Background: Human milk is a rich source of human milk oligosaccharides (HMOs) and bacteria. It is unclear how these components interact within the breast microenvironment.

Objectives: The objectives were first, to investigate the association between maternal characteristics and HMOs, and second, to assess the association between HMOs and microbial community composition and predicted function in milk from women with high rates of gestational glucose intolerance.

Methods: This was an exploratory analysis of a previously completed prospective cohort study (NCT01405547) where milk samples (n = 107) were collected at 3 mo postpartum. Milk microbiota composition was analyzed by V4-16S ribosomal RNA gene sequencing and HMOs by rapid high-throughput HPLC. Data were stratified and analyzed by maternal secretor status phenotype and associations between HMOs and microbiota were determined using linear regression models (ɑ-diversity), Adonis (B-diversity), Poisson regression models (differential abundance), and general linear models (predicted microbial function).

Results: Prepregnancy BMI, race, and frequency of direct breastfeeding, but not gestational glucose intolerance, were found to be significantly associated with a number of HMOs among secretors and non-secretors. Fucosyllacto-N-hexaose was negatively associated with microbial richness (Chao1) among secretors [B-estimate (SE): -9.3 × 102 (3.4 × 102); P = 0.0082] and difucosyllacto-N-hexaose was negatively associated with microbiota diversity (Shannon index) [-1.7 (0.78); P = 0.029] among secretors. Lacto-N-neotetraose (LNnT) was associated with both microbial B-diversity (weighted UniFrac R2 = 0.040, P = 0.036) and KEGG ortholog B-diversity (Bray-Curtis R2 = 0.039, P = 0.043) in secretors. Additionally, difucosyllactose in secretors and disialyllacto-N-hexaose and LNnT in non-secretors were associated with enrichment of predicted microbial genes encoding for metabolism- and infection-related pathways (P-false discovery rate < 0.1).

Conclusions: HMOs are associated with the microbial composition and predicted microbial functions in human milk at 3 mo postpartum. Further research is needed to investigate the role these relations play in maternal and infant health.

Julia K. Copeland, Gary Chao, Shelley Vanderhout, Erica Acton, Pauline W. Wang, Eric I. Benchimol, Ahmed El-Sohemy, Ken Croitoru, Jennifer L. Gommerman, David S. Guttman & the GEMINI Research Team

Gut Microbes 2021 Jan-Dec;13(1):1-29. doi: 10.1080/19490976.2021.1902705.

PMID: 33794735

Abstract

South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.