Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome by Abubucker, Sahar, Segata, Nicola, Goll, Johannes, Schubert, Alyxandria M., Izard, Jacques, Cantarel, Brandi L., Rodriguez-Mueller, Beltran, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T., Methe, Barbara, Schloss, Patrick D., Gevers, Dirk, Mitreva, Makedonka, Huttenhower, Curtis

“…This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.…”
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The origin of methanethiol in midocean ridge hydrothermal fluids by Reeves, Eoghan, McDermott, Jill Marie, Seewald, Jeffrey S.

“…Widespread thermal degradation of subsurface organic matter may be an important source of organic production in unsedimented hydrothermal systems and may influence microbial metabolic strategies in cooler near-seafloor and plume habitats.…”
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Different Quality Classes of Decomposing Plant Residues Influence Dissolved Organic Matter Stoichiometry Which Results in Different Soil Microbial Processing by Ratanaporn Poosathit, Benjapon Kunlanit, Frank Rasche, Patma Vityakon

“…A long-term field experiment was used to explore the effect of the annual application of residues of different quality classes on decomposition processes, focusing on the effects of DOC, DN, and the ratio on the microbial metabolic quotient (<i>q</i>CO₂), which is the inverse of CUE. …”
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Characterization of Functional Microorganisms in Representative Traditional Fermented Dongcai from Different Regions of China by Yanbing Jiang, Hao Fu, Meng Li, Changtao Wang

“…Predictions of microbial metabolic function reveal that carbohydrates, amino acids, polyketides, lipids, and other secondary metabolites are abundantly available for biosynthesis. …”
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Formation of authigenic minerals during microbial degradation in artificial marine media by Joss, Matthew Albert Henry

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Engineering the human gut microbiome through personalized dietary interventions by Nguyen, Le Thanh Tu.

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Phosphorite generative processes around the Precambrian-Cambrian boundary in South China: An integrated study of Mo and phosphate O isotopic compositions by Haiying Yang, Jiafei Xiao, Yong Xia, Zhuojun Xie, Qinping Tan, Jianbin Xu, Shan He, Shengwei Wu, Xiqiang Liu, Xingxiang Gong

“…Based on this data set, we developed a phosphogenic model illustrating formation of these two phosphorite deposits, wherein the Lower Doushantuo phosphorite formed through the reworking of pre-existing phosphatic sediments in anoxic and abiotic ocean, whereas the Upper Doushantuo and Gezhongwu phosphorite formed via microbial metabolisms in oxic and biotic conditions. Our study has implications on the PC/C phosphorite generative processes, as well as paleoenvironmental conditions.…”
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<i>Bifidobacterium animalis</i> subsp. <i>lactis</i> BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome by Daniel Merenstein, Claire M. Fraser, Robert F. Roberts, Tian Liu, Silvia Grant-Beurmann, Tina P. Tan, Keisha Herbin Smith, Tom Cronin, Olivia A. Martin, Mary Ellen Sanders, Sean C. Lucan, Maureen A. Kane

“…Evidence in humans that probiotics may enhance the recovery of microbiota populations after antibiotic treatment is equivocal, and few studies have addressed if probiotics improve the recovery of microbial metabolic function. Our aim was to determine if <i>Bifidobacterium animalis</i> subsp. …”
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Short-Term Effects of Bamboo Biochar and Oyster Shell Powder on Soil Organic Carbon Fraction, Microbial Respiration, and Enzymatic Stoichiometry in a Lei Bamboo Plantation by Haonan Ji, Gensheng Yuan, Yang Liu, Jinzhu Yu, Songhao Li, Qifeng Wu, Hua Qin, Junhui Chen

“…Structural equation modeling indicated that T enhanced soil microbial respiration through increasing soil pH and enzyme activity, while biochar co-addition weakened the stimulation of T on microbial respiration by increasing soil recalcitrant C pool size and microbial metabolic quotient. Our study suggests that adding bamboo biochar together with oyster shell powder could be a better strategy to decrease soil C loss and ameliorate soil acidity in bamboo plantations compared with the application of oyster shell powder alone.…”
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N/S element transformation modulating lithospheric microbial communities by single-species manipulation by Shun Yao, Tianzhi Jin, Lu Zhang, Yong Zhang, Rui Chen, Qian Wang, Mingjie Lv, Chuxiao Hu, Ting Ma, Wenjie Xia

“…Conclusions The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. …”
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Synergy of Dietary Quercetin and Vitamin E Improves Cecal Microbiota and Its Metabolite Profile in Aged Breeder Hens by Felix Kwame Amevor, Zhifu Cui, Xiaxia Du, Jing Feng, Gang Shu, Zifan Ning, Dan Xu, Xun Deng, Weizhen Song, Youhao Wu, Xueqing Cao, Shuo Wei, Juan He, Fanli Kong, Xiaohui Du, Yaofu Tian, Benjamin Karikari, Diyan Li, Yan Wang, Yao Zhang, Qing Zhu, Xiaoling Zhao

“…In the present study, the synergistic effects of quercetin (Q) and vitamin E (E) on cecal microbiota composition and function, as well as the microbial metabolic profile in aged breeder hens were investigated. …”
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Probiotics synergized with conventional regimen in managing Parkinson’s disease by Hairong Sun, Feiyan Zhao, Yuanyuan Liu, Teng Ma, Hao Jin, Keyu Quan, Bing Leng, Junwu Zhao, Xiaoling Yuan, Zhenguang Li, Fang Li, Lai-Yu Kwok, Shukun Zhang, Zhihong Sun, Jinbiao Zhang, Heping Zhang

“…Taken together, Probio-M8 synergized with the conventional regimen and strengthened the clinical efficacy in managing PD, accompanied by modifications of the host’s gut microbiome, gut microbial metabolic potential, and serum metabolites.…”
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Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure by Abigail L. Zeamer, Marie-Claire Salive, Xinming An, Francesca L. Beaudoin, Stacey L. House, Jennifer S. Stevens, Donglin Zeng, Thomas C. Neylan, Gari D. Clifford, Sarah D. Linnstaedt, Scott L. Rauch, Alan B. Storrow, Christopher Lewandowski, Paul I. Musey, Phyllis L. Hendry, Sophia Sheikh, Christopher W. Jones, Brittany E. Punches, Robert A. Swor, Lauren A. Hudak, Jose L. Pascual, Mark J. Seamon, Erica Harris, Claire Pearson, David A. Peak, Roland C. Merchant, Robert M. Domeier, Niels K. Rathlev, Brian J. O’Neil, Paulina Sergot, Leon D. Sanchez, Steven E. Bruce, Ronald C. Kessler, Karestan C. Koenen, Samuel A. McLean, Vanni Bucci, John P. Haran

“…Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. …”
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Cyberlindnera jadinii Yeast as a Protein Source for Weaned Piglets—Impact on Immune Response and Gut Microbiota by Leidy Lagos, Alexander Kashulin Bekkelund, Adrijana Skugor, Ragnhild Ånestad, Caroline P. Åkesson, Charles McL. Press, Margareth Øverland

“…Analysis of predicted microbial metabolic pathways analysis revealed significant upregulation of short-chain fatty acids, ether lipid metabolisms, secondary bile acids, and several other important biosynthesis pathways in cecum and colon of pigs fed yeast. …”
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Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics by J. M. Fadum, M. A. Borton, R. A. Daly, K. C. Wrighton, E. K. Hall

“…This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. …”
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Microbial activity contributes to spatial heterogeneity of wetland methane fluxes by Wyatt Arnold, Meghan Taylor, Mark Bradford, Peter Raymond, Jordan Peccia

“…As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland—both horizontally and vertically—may help explain observed variances in flux. …”
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Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands by Karla Vasco, Nataly Guevara, Juan Mosquera, Sonia Zapata, Lixin Zhang

“…Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome. …”
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Co-Culture of White Rot Fungi <i>Pleurotus ostreatus</i> P5 and <i>Bacillus amyloliquefaciens</i> B2: A Strategy to Enhance Lipopeptide Production and Suppress of Fusarium Wilt of... by Man Xu, Ying Shi, De-Ling Fan, Yi-Jin Kang, Xin-Li Yan, Hong-Wei Wang

“…Co-culture filtrate treatment significantly enhanced the microbial metabolic activity and decreased the abundance of FOC in the rhizosphere soil. …”
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A tale of two theories, a chronosequence and a bioindicator of soil quality by Wardle, David A., Ghani, Anwar

“…In this Citation Classics commentary, we reflect upon a paper that we published in Soil Biology & Biochemistry in 1995 and that provided a critical assessment of the use of the microbial metabolic quotient (qCO2 or the ratio of microbial respiration to biomass) as a bioindicator of soil quality. …”
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Molecular structure of dissolved organic carbon in a sandy soil receiving contrasting quality organic residues by Ratanaporn Poosathit รัตนาพร ภูสถิตย์, Patma Vityakon ปัทมา วิตยากร, Benjapon Kunlanit เบ็ญจพร กุลนิตย์, Frank Rasche

“…During the later stage, topsoil DOC-polysaccharides were negatively related to microbial metabolic quotient (qCO2) (R2 = 0.938). This relationship led to our hypothesis that the dominant source of DOC-polysaccharides, particularly in the TM treatment, was of microbial origin. …”
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