Journal: Heliyon

Article Title: Wood biochar enhances methanogenesis in the anaerobic digestion of chicken manure under ammonia inhibition conditions

doi: 10.1016/j.heliyon.2023.e21100

Figure Lengend Snippet: The effect of control treatment (S + CM), wood biochar treatment (S + CM + BC) and treated biochar treatment (S + CM + TBC) on Richness, Shannon Diversity and Pielou Evenness indices of the microbial communities obtained from the day 40 digestates, in comparison to that of the day 0 feedstock (d0 S + CM).

Article Snippet: Furthermore, the Analysis of Compositions of Microbiomes with Bias Correction 2 package (ANCOM-BC2) was employed to determine the statistical significance between bacterial and archaeal abundances at a significance level of p < 0.05, with p-values altered by the Holm-Bonferroni method, all within R Studio.

Techniques: Control, Comparison

Journal: International Journal of Molecular Sciences

Article Title: Leaf Bacteriome in Sugar Beet Shows Differential Response against Beet curly top virus during Resistant and Susceptible Interactions

doi: 10.3390/ijms23158073

Figure Lengend Snippet: Proposed role of leaf-bacterial-microbiome-mediated sugar beet resistance against beet curly top virus in the virus-resistant genotypes.

Article Snippet: The metagenomic reads were processed using the LC Sciences microbiome data analysis pipeline (LC Sciences, Houston, TX, USA).

Techniques: Virus

Journal: BMC Pediatrics

Article Title: The effect of cesarean delivery on the neonatal gut microbiome in an under-resourced population in the Bronx, NY, USA

doi: 10.1186/s12887-024-04908-7

Figure Lengend Snippet: Gut microbiome diversity increases from birth to 2 years of age. 16 S ribosomal RNA sequencing and analysis were performed as described in the Methods. Chao1 ( P = 2.85E-06, birth vs. 6 months; P = 0.032, 6 vs. 12 months; P = 0.029, 12 vs. 24 months, Panel A) and Shannon ( P = 2.60E-07, birth vs. 6 months; P = 0.15, 6 vs. 12 months; P = 0.07, 12 vs. 24 months, Panel B) plots of alpha diversity of gut microbiome from birth to age 2. Statistical significance was determined by Kruskall Wallis testing

Article Snippet: Stool samples were sent to CD Genomics (Shirley, NY, USA) for gut microbiome analysis, as previously described [ ].

Techniques: RNA Sequencing

Journal: BMC Pediatrics

Article Title: The effect of cesarean delivery on the neonatal gut microbiome in an under-resourced population in the Bronx, NY, USA

doi: 10.1186/s12887-024-04908-7

Figure Lengend Snippet: Gut microbial communities shift dramatically from birth to 2 years of age. Abundance histograms showing beta diversity between different timepoints from birth to age 2. Each bar represents the total sum of the microorganisms in all the fecal samples collected at one timepoint (birth, 6 months, 1 year or 2 years, as indicated). Each color represents a taxonomy, and the length of each color block represents the proportion of the relative abundance of the taxonomy. Four different taxonomic classification levels are shown: phylum ( A ), class ( B ), order ( C ) and family ( D ). Statistically significant differences in the abundance of specific organisms at different timepoints were found by ANCOM, as described in section

Article Snippet: Stool samples were sent to CD Genomics (Shirley, NY, USA) for gut microbiome analysis, as previously described [ ].

Techniques: Blocking Assay

Journal: BMC Pediatrics

Article Title: The effect of cesarean delivery on the neonatal gut microbiome in an under-resourced population in the Bronx, NY, USA

doi: 10.1186/s12887-024-04908-7

Figure Lengend Snippet: Mode of delivery affects the composition of gut microbial communities at birth. Abundance histograms showing beta diversity between samples collected from neonates born by vaginal vs. Cesarean delivery. Each bar represents the total sum of the microorganisms in all the fecal samples collected from neonates who were born by either mode of delivery at one timepoint as shown: birth ( A ), 6 months ( B ), 1 year ( C ) or 2 years ( D ). Three different taxonomic classification levels (phylum, order, family) are shown for birth and 6 months; one taxonomic level (family) is shown for 1 year and 2 years. Increases in organisms in the Burkholderiales order and in the Neisseriacea family in Cesarean deliveries were statistically significant (W = 14 and 86, respectively, by ANCOM, Panel A .) No significant differences were found at 6, 12, or 24 months (Panels B-D )

Article Snippet: Stool samples were sent to CD Genomics (Shirley, NY, USA) for gut microbiome analysis, as previously described [ ].

Techniques:

Journal: BMC Pediatrics

Article Title: The effect of cesarean delivery on the neonatal gut microbiome in an under-resourced population in the Bronx, NY, USA

doi: 10.1186/s12887-024-04908-7

Figure Lengend Snippet: PCoA shows partial separation of the gut microbial communities based on mode of delivery. Unweighted ( A ) and weighted ( B ) PCoA of gut microbiome based on vaginal vs. Cesarean delivery

Article Snippet: Stool samples were sent to CD Genomics (Shirley, NY, USA) for gut microbiome analysis, as previously described [ ].

Techniques:

Journal: BMC Pediatrics

Article Title: The effect of cesarean delivery on the neonatal gut microbiome in an under-resourced population in the Bronx, NY, USA

doi: 10.1186/s12887-024-04908-7

Figure Lengend Snippet: KEGG analysis of Cesarean vs. vaginally delivered microbiomes. Significantly differentially expressed pathways are shown at birth ( A ), 6 months ( B ), 1 year ( C ) and 2 years ( D )

Article Snippet: Stool samples were sent to CD Genomics (Shirley, NY, USA) for gut microbiome analysis, as previously described [ ].

Techniques: