Plant Microbiome {51111201}

Shared Reference Notes

• [1.1] 
  - Cultivation-independent 16S rRNA gene V3/V3–V4 amplicon profiling on 40-year-old grape cell/callus tissues revealed a high bacterial diversity (>250 genera), predominantly Proteobacteria, succeeded by Firmicutes, Actinobacteria, Bacteriodetes, Planctomycetes, and 20 other phyla, including several candidate phyla.
• [1.2] [#Plant-based diet] 
  - several putative short-chain fatty acid (SCFA) fermenters associated with eating more than 30 types of plants, including sOTUs putatively of the species Faecalibacterium prausnitzii and of the genus Oscillospira. - Because bacteria differ in their carbohydrate binding modules and enzymes that hydrolyze diverse substrates in the gut (28), a diet containing various types of dietary fibers and resistant starches likely supports a more diverse microbial community. - Individuals who consume more than 30 types of plants per week compared to those who consume 10 or fewer plants per week had significantly reduced abundance of antibiotic resistance genes for aminoglycosides, chloramphenicol, and major facilitator superfamily (MFS) transporters (antibiotic efflux pumps).
• [1.3] [#Molecular patterns] 
  - Antigenic microbial debris as MAMPs in certain botanical supplements are immune stimulants, liken to vaccines adjuvants. - large number of plants to discern > high concentration of bio-active MAMPS. - 65 out of 2000+ tested with high TLR4 agonist MAMP presence and investigate the plant vs. the microbiome.
• [1.4] [#High fibre plant protein-rich diet, #Plant-based diet] 
  - #Prevotella thrives on plant- or fiber-rich diets. - These include diets commonly described as non-Western, Mediterranean, or rural African diet.
• [1.5] 
  - to the presence of #Oxygen in the newborn gut,Citation37 facultative anaerobic #Gammaproteobacteria i.e., #Pantoea, #Erwinia, and #Acinetobacter which originate from fruit and vegetables can colonize in the gut of #Infants during the early weaning period.
• [#Human gammaherpesvirus 4] - fruit and vegetables associated bacteria found in the human gut were dominated by the bacterial orders #Enterobacterales (mean of relative abundance 20.1% in children and mean of relative abundance 22.5% in adults), #Burkholderiales (mean of relative abundance 7.4% in children and mean of relative abundance 9.1% in adults), #Actinomycetales (mean of relative abundance 7.8% in children and mean of relative abundance 7.6% in adults) and #Lactobacillales (mean of relative abundance 11.9% in children and mean of relative abundance 8.5% in adults) which were represented by the bacterial genera #Erwinia, #Lactococcus, #Enterobacter, and #Microbacterium
• - a gene encoding #Acetate kinase (ackA) was detected in 71 MAGs mostly affilitated to #Actinomycetales or #Enterobacterales.
• - genes involved in #Vitamin K2 biosynthesis, i.e., menABCDEF, were also detected in MAGs assigned to the bacterial orders #Actinomycetales, #Pseudomonadales, and Propionibacteriales.
• - 31 genera, including #Pseudomonas, #Sphingomonas, #Aeromicrobium, and #Pantoea had representatives in both the human gut and the fruit and vegetable microbiomes.
• - 79 genera, including #Microbacterium, #Nocardioides, and #Brevundimonas, could only be constructed from fruit and vegetable samples and not from human gut metagenome samples.
• - Genes encoding #Propionate CoA-transferase and #Butyrate kinase that are involved in #Propionate and #Butyrate biosynthesis, respectively, were only detected in a small number of MAGs that belong to #Burkholderiales and #Rhizobiales.
• - fruit- and vegetable-associated bacteria were consistently present at a low abundance in the human gut.
• - The abundance of fruit- and vegetable-associated bacteria ranged between 0.004% and 3.604% in the gut microbiome of children and 0.003–3.122% in the gut microbiome of adults
• - 128 MAGs harbored the cobC gene that encodes a cobalamin (#Vitamin B12) biosynthetic protein. This gene was highly prevalent in MAGs that belong to the bacterial orders #Sphingomonadales (44.8%), #Rhizobiales (46.4%), and #Pseudomonadales (34.6%).

References Notes