Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles

Rao, Manik Prabhu Narsing; Luo, Zhen-Hao; Dong, Zhou-Yan; Li, Qi; Liu, Bingbing; Guo, Shuxian; Nie, Guo-Xin; Li, Wen‐Jun

doi:10.1016/j.envres.2022.112888

Cited by 50 publications

(11 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In another study regarding lung cancer, the relative content of Chloroflexi phylum was elevated in cancerous tissue samples compared to paracancerous tissue samples ( Zhou et al, 2023 ). Currently, the biochemical roles of the Chloroflexi phylum, such as carbon fixation, carbon monoxide oxidation, nitrogen, and sulfur metabolism, have been gradually revealed ( Narsing Rao et al, 2022 ). It has also been demonstrated that the Chloroflexi phylum has a nitrate reductase gene ( Sanford et al, 2012 ; McIlroy et al, 2016 ; Narsing Rao et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…Currently, the biochemical roles of the Chloroflexi phylum, such as carbon fixation, carbon monoxide oxidation, nitrogen, and sulfur metabolism, have been gradually revealed ( Narsing Rao et al, 2022 ). It has also been demonstrated that the Chloroflexi phylum has a nitrate reductase gene ( Sanford et al, 2012 ; McIlroy et al, 2016 ; Narsing Rao et al, 2022 ). Nitrite is further reduced to NO by nitrate reductase.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

The relationship between gastric microbiome features and responses to neoadjuvant chemotherapy in gastric cancer

Zhang,

Xu,

Zhou

2024

Front. Microbiol.

View full text Add to dashboard Cite

BackgroundEmerging evidence demonstrates that the gastrointestinal microbiome has the potential to be a biomarker in neoadjuvant chemoradiotherapy for colorectal cancer (CRC). Yet studies on the impact of the gastric microbiome (GM) on the response to neoadjuvant chemotherapy (NACT) are still scarce.MethodsForty-eight patients with gastric cancer participated in this retrospective study, and 16S rRNA sequencing was performed to evaluate formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens and fresh-frozen tissues.ResultsIn this study, 16 bacterial taxa at different levels, including Bacillus, Anaerococcus, and Chloroflexi, were identified to be enriched before NACT in response (R) patients in group FFPE. In contrast, 6 bacterial taxa, such as Haemophilus, Veillonellaceae (Veillonella), etc. were enriched after NACT, in which we reported for the first time that the phylum Chloroflexi was enriched before NACT in R patients. Thirty-one bacterial taxa of Coriobacteriaceae, Ruminococcaceae, Veillonellaceae, and Lachnospiraceae were identified in group mucosa as being enriched in R patients. In comparison, 4 bacterial taxa dominated by the phylum Proteobacteria were enriched in NR patients. Notably, the family Veillonellaceae was found in both tissue samples, and the metabolic pathways, including the citrate cycle (TCA cycle) and various amino acids, including alanine, were found to be potentially predictive in both sample species.ConclusionThere are differences in the features of the GM for different NACT response results. The causal relationship deserves to be confirmed by further investigations.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The relationship between gastric microbiome features and responses to neoadjuvant chemotherapy in gastric cancer

Zhang,

Xu,

Zhou

2024

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Furthermore, the present study identified that tree and shrub alpha diversities were significantly related to Chloroflexi in the CK group. Chloroflexi has a highly diverse nutritional pattern and is involved in the biogeochemical cycle of elements (Narsing Rao et al, 2022). Therefore, the high level of Chloroflexi may be a fundamental reason for promoting the differentiation of apex communities.…”

Section: Discussionmentioning

confidence: 99%

“…Chloroflexi has a highly diverse nutritional pattern and is involved in the biogeochemical cycle of elements (Narsing Rao et al, 2022).…”

Section: Relationships Of Microbial Communities With Soil Properties ...mentioning

confidence: 99%

Distinctive patterns of soil microbial community during forest ecosystem restoration in southwestern China

Zuo

Liu

et al. 2023

Land Degrad Dev

View full text Add to dashboard Cite

Microorganisms are essential in soil biogeochemical processes and vegetation establishment. Nonetheless, investigating predictable patterns in the microbial structure during forest restoration damaged by natural or human factors in southwestern China is still limited. Hence, the study intended to explore the effects of forest restoration damaged by illegal construction, abandoned mines, and meteorological disasters on the microbial structure and its consequence on ecosystem functioning. The results uncovered that soil and plant attributes in the restoration forests damaged by illegal construction were similar to the natural community. Furthermore, the alpha diversity indexes were higher in the restoration forests damaged by human factors than in the natural community. Co‐occurrence network analysis identified hub bacterial (e.g., Roseiarcus and Comamonas) and fungal (e.g., Exophiala and Botryotrichum) taxa, proving densely connected interactions with other microorganisms. Restoration forests damaged by illegal construction harbored beneficial genera belonging to Proteobacteria (Nordella, Xanthobacteraceae, and Sphingomonas) and Basidiomycota (Panaeolus, Psilocybe, and Sebacina), whereas restoration forests damaged by abandoned mines presented specialized bacteria involved in dark sulfur oxidation and ureolysis. Correlation analysis showed that soil properties, especially water content and pH, were the dominant factors affecting the microbial communities. Tree and shrub alpha diversities were significantly related to Chloroflexi in the natural community, and herbaceous richness was remarkably related to Proteobacteria and Mortierellomycota in the restoration forest damaged by human factors. Collectively, this comprehensive analysis generates novel insights to explore the contrasting responses of microbial communities during the process of restoration and provides essential microbial indicators for habitat restoration in southwestern China.

show abstract

“…Actinobacteriota includes important saprophytic bacteria that can promote the decay of plant and animal remains in soil and play a role in the nitrogen cycle in soil ( Hazarika et al, 2022 ). Chloroflexi is a class of photoautotrophic bacteria known for their special 3-HP fixed CO 2 , making these bacteria of great significance to the entire ecosystem as primary producers ( Narsing et al, 2022 ). Proteobacteria is the largest and most diverse phylum of bacteria and is of extensive importance in terms of phylogeny, ecology, and pathogenicity ( Feng L. et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Chen

Qin³

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

IntroductionThe continuous application of cow manure in soil for many years leads to the accumulation of heavy metals, pathogenic microorganisms, and antibiotic resistance genes. Therefore, in recent years, cow manure has often been mixed with botanical oil meal as organic fertilizer applied to farmland to improve soil and crop quality. However, the effects of various botanical oil meal and cow manure mixed organic fertilizers on soil microbial composition, community structure, and function, tobacco yield, and quality remain unclear.MethodsTherefore, we prepared organic manure via solid fermentation by mixing cow manure with different oil meals (soybean meal, rape meal, peanut bran, sesame meal). Then, we studied its effects on soil microbial community structure and function, physicochemical properties, enzyme activities, tobacco yield and quality; then we analyzed the correlations between these factors.Results and discussionCompared with cow manure alone, the four kinds of mixed botanical oil meal and cow manure improved the yield and quality of flue-cured tobacco to different degrees. Peanut bran, which significantly improved the soil available phosphorus, available potassium, and NO3–-N, was the best addition. Compared with cow manure alone, soil fungal diversity was significantly decreased when rape meal or peanut bran was combined with cow manure, while soil bacterial and fungal abundance was significantly increased when rape meal was added compared with soybean meal or peanut bran. The addition of different botanical oil meals significantly enriched the subgroup_7 and Spingomonas bacteria and Chaetomium and Penicillium fungi in the soil. The relative abundances of functional genes of xenobiotics biodegradation and metabolism, soil endophytic fungi, and wood saprotroph functional groups increased. In addition, alkaline phosphatase had the greatest effect on soil microorganisms, while NO3–-N had the least effect on soil microorganisms. In conclusion, the mixed application of cow manure and botanical oil meal increased the available phosphorus and potassium contents in soil; enriched beneficial microorganisms; promoted the metabolic function of soil microorganisms; increased the yield and quality of tobacco; and improved the soil microecology.

show abstract

Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles

Cited by 50 publications

References 71 publications

The relationship between gastric microbiome features and responses to neoadjuvant chemotherapy in gastric cancer

The relationship between gastric microbiome features and responses to neoadjuvant chemotherapy in gastric cancer

Distinctive patterns of soil microbial community during forest ecosystem restoration in southwestern China

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Contact Info

Product

Resources

About