Article
Microbiology
Eleni Kamilari, Marina Efthymiou, Dimitrios A. Anagnostopoulos, Dimitrios Tsaltas
Summary: The research utilized high-throughput sequencing to analyze the bacterial diversity of traditional Cyprus sausages from the Troodos mountainous region of Pitsilia and industrially produced sausages. The findings showed that Pitsilia sausages had significantly higher bacterial diversity, suggesting that microbial communities could serve as an additional tool for identifying the authenticity of Cypriot sausages.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Yuntian Xin, Jingxian Xie, Bingru Nan, Chen Tang, Yunshan Xiao, Quanfeng Wu, Yi Lin, Xueqin Zhang, Heqing Shen
Summary: This study aimed to improve the efficiency of bacterial DNA extraction from meconium, a challenging process due to low microflora levels and PCR inhibitors. Using freeze-thawing cycles and different freezing conditions, the researchers found that freezing at -20 degrees Celsius was the best condition for DNA extraction and preservation of microbial diversity in meconium. The developed protocol could significantly enhance DNA extraction efficiency and preserve the species diversity of meconium microflora, providing potential benefits for newborn bacterial colonization studies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Engineering, Chemical
Edyta Juszczuk-Kubiak, Agnieszka Dekowska, Barbara Sokolowska, Marzena Polaska, Krzysztof Lendzion
Summary: This study evaluated the development of spoilage-related bacterial profiles in chilled ostrich meat under vacuum packaging by using culture-dependent and 16S rDNA amplicon sequencing methods. The results showed that Photobacterium and lactic acid bacteria were the most prevalent genera in vacuum-packaged ostrich meat.
Article
Microbiology
Matheus Rodrigo Iossi, Isabela Arruda Palu, Douglas Moraes Soares, Wagner G. Vieira, Lucas Silva Alves, Cassius Stevani, Cinthia E. C. Caitano, Samir V. F. Atum, Renato S. Freire, Eustaquio S. Dias, Diego Cunha Zied
Summary: This study evaluated the influence of mushroom-colonized compost extract (MCCE) prepared with different soaking times on the cultivation of Agaricus subrufescens. It was found that longer soaking time led to a decrease in bacterial diversity in MCCE. The application of 24 h soaked MCCE resulted in increased biological efficiency, precociousness, number of mushrooms, and mushroom weight.
Article
Agriculture, Dairy & Animal Science
Hu Liu, Hui Jiang, Lizhuang Hao, Xuliang Cao, Allan Degen, Jianwei Zhou, Chengfu Zhang
Summary: Supplementary feed alters the composition of rumen microbiota and concentrations of ruminal volatile fatty acids in lactating yaks, demonstrating its potential to manipulate the rumen microbiota composition.
Article
Microbiology
Ming-Yi Chou, Trine B. Andersen, Marco E. Mechan Llontop, Nick Beculheimer, Alassane Sow, Nick Moreno, Ashley Shade, Bjoern Hamberger, Gregory Bonito
Summary: This study investigates the effects of different terpenes on belowground bacterial and fungal microbiomes. The research finds that terpene applications have significant and variable impacts on bacterial and fungal communities, but these impacts are localized to the artificial root system and the fungal rhizosphere. The study also reveals the varying effects of terpenes on individual microbial isolates and demonstrates the complexity of microbe-terpene interactions in the rhizobiome.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agriculture, Dairy & Animal Science
P. Papademas, E. Kamilari, M. Aspri, D. A. Anagnostopoulos, P. Mousikos, A. Kamilaris, D. Tsaltas
Summary: The study found that donkey milk has high microbiological quality without significant food-borne pathogens. High-throughput sequencing revealed that donkey milk is mainly composed of gram-negative bacteria including lactic acid bacteria.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Veterinary Sciences
Huan Chen, Han Yan, Yan Xiu, Linlin Jiang, Jianlong Zhang, Guozhong Chen, Xin Yu, Hongwei Zhu, Xiaoyu Zhao, Youzhi Li, Wenli Tang, Xingxiao Zhang
Summary: The study found that the concentration of bacterial aerosols in the broiler house varied significantly in different seasons, with the highest concentration in summer and the lowest in winter. The composition of bacterial species also varied by season, with a higher proportion of Gram-negative bacteria in autumn. Additionally, the structure of potential pathogenic bacterial genera differed by season.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Ming-Yi Chou, Trine B. Andersen, Marco E. Mechan Llontop, Nick Beculheimer, Alassane Sow, Nick Moreno, Ashley Shade, Bjoern Hamberger, Gregory Bonito
Summary: This study investigates the effects of different terpenes on plant microbiomes belowground. The results show that terpene applications have significant impacts on bacterial and fungal communities, but these effects are localized to the artificial root system and fungal rhizosphere. Bioassays on responsive bacteria and fungi isolated from the sorghum rhizobiome validate the direct microbial responses to terpenes. These findings shed light on the complex interactions between terpenes and microorganisms in the rhizobiome.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Applied
Zhengyang Song, Yanzhou Hu, Xu Chen, Guohui Li, Qiding Zhong, Xiaoyun He, Wentao Xu
Summary: This study investigated the correlation between propionic acid production and bacterial community succession during the fermentation of gray sufu. Results showed that Propionibacterium and Lactobacillus played important roles in the production of propionic acid, while Fusobacterium, Providencia, Lactobacillus, and Bacillus were key factors in reducing propionic acid content. This research provides new insights into quality control of traditional fermented foods.
Article
Environmental Sciences
Muyuan Zhang, Weng Liang, Zhineng Tu, Ronghua Li, Zengqiang Zhang, Amjad Ali, Ran Xiao
Summary: The study found that bacterial communities in compost and bamboo biochar additive differed, with compost having higher abundance of bacteria and biochar having higher diversity. Additionally, the dominant phylum Firmicutes decreased in compost samples but remained dominant in biochar additives throughout the composting period. This suggests that biochar addition can impact the bacterial composition and abundance in composting processes.
Article
Microbiology
Fangchao Song, Jennifer V. Kuehl, Arjun Chandran, Adam P. Arkin
Summary: In this study, a direct PCR method was evaluated as a cost-effective and time-saving alternative to traditional DNA extraction methods for analyzing microbial communities. The direct PCR method showed comparable efficiency to the conventional DNeasy PowerSoil protocol, with higher efficiency for extracting gDNA from Gram-negative strains. This method is significantly less expensive and faster, making it a potential solution for high-throughput large-scale bacterial community analysis.
Article
Infectious Diseases
A. Stebner, A. Ensser, W. Geissdoerfer, Y. Bozhkov, R. Lang
Summary: Next-generation sequencing (NGS) using 16S-rRNA was applied for metagenomic analysis of intracranial abscess and meningitis samples, revealing a polymicrobial nature of these infections and demonstrating the suitability of the MiSeq platform for metagenomic diagnostics. The most prevalent bacteria in brain abscesses were Streptococcus intermedius and Fusobacterium nucleatum.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Immunology
Yinghu Chen, Lingfeng Mao, Dengming Lai, Weize Xu, Yuebai Zhang, Sihao Wu, Di Yang, Shaobo Zhao, Zhicong Liu, Yi Xiao, Yi Tang, Xiaofang Meng, Min Wang, Jueliang Shi, Qixing Chen, Qiang Shu
Summary: We developed a rapid and low-cost method for 16S rDNA nanopore sequencing by adding barcodes to the 16S primer. The accuracy rate for identifying common pulmonary pathogens was 100% and the turnaround time was shortened to 6-8 hours. By comparing the results with culture or PCR, the method showed high consistency in terms of sensitivity and specificity.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Horticulture
Minkai Yang, Zhongling Wen, Chenyu Hao, Aliya Fazal, Yonghui Liao, Fuhe Luo, Weixuan Yao, Tongming Yin, Rongwu Yang, Jinliang Qi, Zhi Hong, Guihua Lu, Yonghua Yang
Summary: The study showed that the EPSPS/GAT dual transgenic soybean line Z106 and glyphosate application have minimal effect on the composition of the soybean rhizosphere bacterial community, but at the seed filling and maturing stages, Z106 had a higher proportion of nitrogen-fixing rhizobium Ensifer fredii compared to ZH10 and Z106G.
Article
Environmental Sciences
Reda A. Abou-Shanab, Cara M. Santelli, Michael J. Sadowsky
Summary: The study showed that certain soil bacteria can enhance the availability of arsenic in soil, thus increasing arsenic uptake by Pteris vittata plants. Specific bacterial strains significantly improved arsenic uptake by P. vittata, leading to higher bioconcentration factors and potential use in large-scale soil remediation.
INTERNATIONAL JOURNAL OF PHYTOREMEDIATION
(2022)
Article
Geosciences, Multidisciplinary
Weibo Kong, Fuyuan Su, Qian Zhang, Satoshi Ishii, Michael J. Sadowsky, Samiran Banerjee, Mingan Shao, Liping Qiu, Xiaorong Wei
Summary: This study in the Loess Plateau of China reveals that soil erosion and deposition have significant impacts on bacterial communities and multifunctionality. Erosion reduces bacterial richness and multifunctionality, but deposition can alleviate these negative effects. The study suggests that sustainable soil management and restoration of degraded lands can benefit from understanding the interactions between erosion, deposition, bacterial communities, and soil multifunctionality.
Article
Dentistry, Oral Surgery & Medicine
Ronald Ordinola-Zapata, Dina Mansour, Flavia Saavedra, Christopher Staley, Ruoqiong Chen, Alex S. Fok
Summary: This study aimed to assess the effectiveness of a non-instrumentation technique in disinfecting root canals infected by a human dental plaque-derived multispecies biofilm. The results showed that the non-instrumentation technique led to significant changes in the composition of the root canal microbiota, and its impact on the microbiota was greater compared to the conventional cleaning technique.
INTERNATIONAL ENDODONTIC JOURNAL
(2022)
Article
Environmental Sciences
Jeonghwan Jang, Valery E. Forbes, Michael J. Sadowsky
Summary: This study discovered the presence of Cutibacterium acnes strains in the gut microbiota of the marine polychaete Capitella teleta. These strains produce propionate and vitamin B-12, which are essential microbial metabolites for the host. C. acnes, as a member of the worm's core functional microbiota, is likely favored by the host gut environment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Environmental Sciences
Warish Ahmed, Stuart L. Simpson, Paul M. Bertsch, Kyle Bibby, Aaron Bivins, Linda L. Blackall, Silvia Bofill-Mas, Albert Bosch, Joao Brandao, Phil M. Choi, Mark Ciesielski, Erica Donner, Nishita D'Souza, Andreas H. Farnleitner, Daniel Gerrity, Raul Gonzalez, John F. Griffith, Pradip Gyawali, Charles N. Haas, Kerry A. Hamilton, Hapuarachchige Chandithal Hapuarachchi, Valerie J. Harwood, Rehnuma Haque, Greg Jackson, Stuart J. Khan, Wesaal Khan, Masaaki Kitajima, Asja Korajkic, Giuseppina La Rosa, Blythe A. Layton, Erin Lipp, Sandra L. McLellan, Brian McMinn, Gertjan Medema, Suzanne Metcalfe, Wim G. Meijer, Jochen F. Mueller, Heather Murphy, Coleen C. Naughton, Rachel T. Noble, Sudhi Payyappat, Susan Petterson, Tarja Pitkanen, Veronica B. Rajal, Brandon Reyneke, Fernando A. Roman, Joan B. Rose, Marta Rusinol, Michael J. Sadowsky, Laura Sala-Comorera, Yin Xiang Setoh, Samendra P. Sherchan, Kwanrawee Sirikanchana, Wendy Smith, Joshua A. Steele, Rosalie Subburg, Erin M. Symonds, Phong Thai, Kevin Thomas, Josh Tynan, Simon Toze, Janelle Thompson, Andy S. Whiteley, Judith Chui Ching Wong, Daisuke Sano, Stefan Wuertz, Irene Xagoraraki, Qian Zhang, Amity G. Zimmer-Faust, Orin C. Shanks
Summary: Monitoring pathogens like SARS-CoV-2 in wastewater using RT-PCR is effective for public health information, but there is a lack of standardized protocols for wastewater surveillance. Key strategies for improving accuracy include QA/QC measures, representative sampling, virus concentration, and clear data interpretation guidelines.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Joao Brandao, Chelsea Weiskerger, Elisabete Valerio, Tarja Pitkanen, Paivi Merilainen, Lindsay Avolio, Christopher D. Heaney, Michael J. Sadowsky
Summary: Beach sand and water are both important for human health and their microbiology has been studied for decades. The World Health Organization recently recommended including recreational beach sands in monitoring for enterococci and Fungi. Global climate change is affecting beach microbial contamination, and the changing world and human travel contribute to the spread of endemic allochthonous microbiota. In the future, alternative microbial standards will be necessary to ensure the health of beach users from both sand and water contaminants.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Letter
Immunology
Armin Rashidi, Jonathan U. Peled, Christopher Staley
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Dentistry, Oral Surgery & Medicine
Ronald Ordinola-Zapata, Massimo Costalonga, Donald Nixdorf, Matthew Dietz, David Schuweiler, Bruno P. Lima, Christopher Staley
Summary: This study evaluated the composition of the root canal microbiome in cases of primary and secondary apical periodontitis. The results showed that primary endodontic infections are more diverse than secondary infections, and the microbial composition is not associated with the clinical manifestations of apical periodontitis.
INTERNATIONAL ENDODONTIC JOURNAL
(2023)
Article
Immunology
Katharine E. Block, Koji Iijima, Mark J. Pierson, Daniel A. Walsh, Rinna Tei, Tamara A. Kucaba, Julie Xu, Mohammad Haneef Khan, Christopher Staley, Thomas S. Griffith, Henry J. McSorley, Hirohito Kita, Stephen C. Jameson
Summary: This study shows that mice initially have impaired innate type 2 responses to lung allergens after exposure to various pathogens, but reactivity resets over time. Cohousing mice for 2 months can restore immune responses to allergens, with interferons playing a regulatory role.
Article
Oncology
Travis J. Gates, Ce Yuan, Mihir Shetty, Thomas Kaiser, Andrew C. Nelson, Aastha Chauhan, Timothy K. Starr, Christopher Staley, Subbaya Subramanian
Summary: Inflammation of the colon (colitis) increases the risk of colorectal cancers, and gut microbiota may be involved in cancer development. Manipulating the bacteria community in the colon could be a potential way to prevent cancer. A study using mice found that transferring bacteria from healthy mice to those with colitis increased the presence of Akkermansia, which may alleviate colon inflammation, while untreated mice had an increase in other bacteria types, such as Anaeroplasma and Alistipes, which could contribute to inflammation. These findings suggest that specific bacteria types may help reduce colon inflammation and prevent cancer.
Article
Biochemistry & Molecular Biology
Yuyin Zhou, Zheting Bi, Matthew J. Hamilton, Li Zhang, Rui Su, Michael J. Sadowsky, Sabita Roy, Alexander Khoruts, Chi Chen
Summary: This study investigated the metabolic changes induced by FMT in rCDI patients through metabolomic analysis of urine samples. The results showed that the concentration of p-cresol sulfate in urine rapidly increased, making it a potential therapeutic indicator for the effectiveness of antibiotics and FMT.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Sonja Boatman, Thomas Kaiser, Harika Nalluri-Butz, Mohammad Haneef Khan, Matthew Dietz, Julia Kohn, Abigail J. Johnson, Wolfgang B. Gaertner, Christopher Staley, Cyrus Jahansouz
Summary: The interaction between host diet and gut microbiota plays a significant role in perioperative complications, particularly anastomotic leak. This study used a murine surgical model to investigate the impact of diet and fecal microbial transplantation (FMT) on the intestinal microbiota and their relationship to anastomotic leak. The results showed that a Western diet leads to dysbiosis in the gut microbiota and increased rates of anastomotic leak, while FMT from healthy donors on a lean diet reduces the risk of anastomotic leak. A microbial index was also developed to predict the occurrence of leak.
Review
Microbiology
Hao Wang, Gary W. Feyereisen, Ping Wang, Carl Rosen, Michael J. Sadowsky, Satoshi Ishii
Summary: This study investigated the effects of bioaugmentation and biostimulation on the microbiomes and nitrate removal rates of woodchip bioreactors (WBRs). The results showed that introducing denitrifying bacteria and adding acetate can enhance the nitrate removal efficiency of WBRs. Additionally, the study found that denitrifiers are unevenly distributed in WBRs.
MICROBIOLOGY SPECTRUM
(2023)
Article
Gastroenterology & Hepatology
Kendall R. McEachron, Harika Nalluri, Gregory J. Beilman, Varvara A. Kirchner, Timothy L. Pruett, Martin L. Freeman, Guru Trikudanathan, Christopher Staley, Melena D. Bellin
Summary: This study found significant differences in gut microbial community structure between patients with CP and healthy controls, with lower gut microbial diversity in CP patients. Among participants with CP, lower gut microbial diversity was associated with more severe functional abdominal symptoms.
Article
Hematology
Abdelrahman Saqr, Brooke Carlson, Christopher Staley, Armin Rashidi, Mahmoud Al-Kofahi, Thomas Kaiser, Shernan Holtan, Margaret MacMillan, Jo-Anne Young, Najla El Jurdi, Daniel Weisdorf, Alexander Khoruts, Pamala A. Jacobson
Summary: Mycophenolate mofetil (MMF) is an important immunosuppressant used after allogeneic hematopoietic cell transplantation (HCT). This study found that blood concentrations of MMF were highly variable, with low concentrations associated with the risk of graft-versus-host disease (GVHD) and high concentrations associated with toxicity. The presence of beta-glucuronidase-producing bacteria in the gastrointestinal tract may enhance the enterohepatic recirculation (EHR) of MMF, leading to higher concentrations. Individuals with high EHR had a greater abundance of certain Bacteroides species in their stool and higher exposure to MMF.
TRANSPLANTATION AND CELLULAR THERAPY
(2022)