Article
Agriculture, Dairy & Animal Science
Xin Song, Lu Liu, Xin-Xin Liu, Zhi-Qiang Xiong, Chun-Liang Xie, Shij-Jie Wang, Lian-Zhong Ai
Summary: This study established a precise and efficient genome editing plasmid for Lactococcus lactis NZ9000 using CRISPR-Cas9 technology, enabling efficient gene deletion and editing. The tool showed high efficiency in gene deletion and sequential gene deletion, providing a new means for further investigation of the L. lactis genome.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Multidisciplinary
Hui Wang, Lianzhong Ai, Yongjun Xia, Guangqiang Wang, Zhiqiang Xiong, Xin Song
Summary: This study designed sgRNAs for Lactococcus lactis NZ9000 LLNZ_RS02020 (ldh) and LLNZ_RS10925 (upp) individually using online prediction software - CRISPOR - and successfully constructed a series of knockout strains to compare the knockout efficiency of each sgRNA and analyze the differences between software predictions and actual experimental results.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Biotechnology & Applied Microbiology
Nathalie N. S. E. Henriksen, Mads Frederik Hansen, Heiko T. Kiesewalter, Jakob Russel, Joseph Nesme, Kevin R. Foster, Birte Svensson, Gunnar Oregaard, Jakob Herschend, Mette Burmolle
Summary: This study shows that cultivation in a structured environment facilitates coexistence, evolution, and adaptation of bacterial communities. Co-cultivation in a biofilm model resulted in stable coexistence of two bacterial species and drove the evolution of high-yield variants. This study emphasizes the importance of structured environments for the cultivation and evolution of industrially important bacterial communities.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biotechnology & Applied Microbiology
Tina Vida Plavec, Tim Kljucevsek, Ales Berlec
Summary: Researchers have successfully developed a modified BglBrick system in Lactococcus lactis, enabling simple and modular construction of multigene plasmids and controlled simultaneous expression of three proteins.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Pavel Yu Pechenov, Danil A. Garagulya, Daniil S. Stanovov, Andrey Letarov
Summary: Lactococcus lactis is an important microorganism used in the industry and research of lactic acid bacteria. The lack of genome-editing tools has hindered the development of improved strains. Researchers recently discovered a CRISPR-Cas-associated transposon system that allows for the editing of the L. lactis genome, enabling the incorporation of large gene fragments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ecology
Rinke J. van Tatenhove-Pel, Tomaz Rijavec, Ales Lapanje, Iris van Swam, Emile Zwering, Jhonatan A. Hernandez-Valdes, Oscar P. Kuipers, Cristian Picioreanu, Bas Teusink, Herwig Bachmann
Summary: Metabolic interactions between cells are influenced by the distance between cells, and in a three-dimensional system, these interactions are constrained by competition or removal of metabolites, reducing the metabolic interaction distances in the low micrometer range.
Article
Food Science & Technology
Rong Wang, Haruyo Nakajima-Adachi, Yimei Wang, Yingyu Zhou, Wenting Gu, Erika Hiraide, Mamiko Morinaga, Ryogo Nakagawa, Shotaro Nakamura, Tomohiro Takano, Xuyang Li, Mayumi Saeki, Osamu Kaminuma, Takachika Hiroi, Kenji Uchida, Hidemasa Motoshima, Masaru Tanokura, Takuya Miyakawa, Satoshi Hachimura
Summary: Lactococcus lactis subsp. cremoris YRC3780 isolated from kefir has anti-allergic effects in humans. The oral administration of L. cremoris YRC3780 enhanced IFN-gamma and IL-12 production, inhibited IL-4 production, and attenuated symptoms in an atopic dermatitis mouse model by regulating cytokine expression.
JOURNAL OF FUNCTIONAL FOODS
(2022)
Article
Biotechnology & Applied Microbiology
Ryutaro Kawai, Yoshihiro Toya, Hiroshi Shimizu
Summary: Combining growth-associated pathway engineering based on FBA and ALE is an effective method to increase the production of useful compounds. This study introduces a novel ALE approach based on mutualistic co-culture, which significantly improves the yield of phenylalanine production.
BIOPROCESS AND BIOSYSTEMS ENGINEERING
(2022)
Article
Microbiology
Yihui Gao, Jiaqing Zhu, Liang Zhao, Lianming Cui, Changcheng Zhao, Juanjuan Yi, Xin Liu, Qiaozhen Kang, Limin Hao, Laizheng Lu, Jike Lu
Summary: This study investigates the protective effects and metabolites of Lactococcus lactis subsp. lactis (L. lactis) in response to UV stress. Results show that L. lactis can adapt to UV stress by adjusting metabolic pathways and producing special metabolites to protect itself. This research contributes to the development of robust strains and provides insights into potential bioprotectants.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Antonio Caivano, Wouter van Winden, Giuliano Dragone, Solange I. Mussatto
Summary: Constraint-based genome-scale models (GEMs) are a powerful tool for predicting and analyzing microbial phenotypes. This study implemented enzymatic constraints into a GEM of Clostridium ljungdahlii, improving the predictive ability of growth rate and product profile. In silico metabolic engineering was then performed to enhance the production of desired fermentation products, resulting in different strategies for overproduction without redundant knockouts. The study highlights the potential of mixotrophic growth for improving cell growth and productivity with CO2 fixation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Agriculture, Multidisciplinary
Bibek Byanju, Swastik Sen, Thomas Mansell, Buddhi P. P. Lamsal
Summary: Corn steep liquor (CSL) and thin stillage were evaluated as growth media for recombinant Lactococcus lactis to produce antifreeze proteins (AFPs). Light CSL and thin stillage were optimized with additives and trace elements to enhance the growth of wild-type and recombinant strains. The fermentation supernatants showed longer times to supercool and freeze, indicating potential use as antifreeze compounds in frozen food and non-food applications.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Multidisciplinary Sciences
Justin Y. Lee, Mark P. Styczynski
Summary: Current metabolic modeling tools have limitations and the Linear Kinetics-Dynamic Flux Balance Analysis (LK-DFBA) framework was developed to address these limitations. The framework captures metabolite dynamics and regulation while retaining a linear programming structure. However, different systems require different constraint approaches, and genetic perturbations do not affect the optimal constraint approach.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loic Pauleve, Anne Siegel
Summary: This study presents a novel approach to infer Boolean rules for metabolic regulation from time-series data and a prior knowledge network (PKN). By combining answer set programming and linear programming, candidate Boolean regulations that can reproduce the given data are generated. The quality of predictions depends on the available time-series data, such as kinetic, fluxomics or transcriptomics data.
Article
Chemistry, Applied
Min Li, Weicheng Li, Dongyu Li, Juanjuan Tian, Luyao Xiao, Lai-Yu Kwok, Wei Li, Zhihong Sun
Summary: Exopolysaccharides (EPSs) from Lactococcus lactis subsp. lactis IMAU11823 were found to have strong reducing power and no cytotoxicity. The EPSs had different sugar compositions and molecular weights, with EPS-1 being a linear structure composed of glucose and mannose, and EPS-2 being a more complex, non-linear structure composed of mannose, glucose, and rhamnose. Furthermore, a biosynthesis model for EPS production in the IMAU11823 strain was proposed. This study broadens the understanding of the formation, structure, and function of complex EPSs produced by Lactococcus lactis subsp. lactis IMAU11823.
Article
Food Science & Technology
Xin Shen, Weicheng Li, Hongyu Cai, Shuai Guo, Min Li, Yangshuo Liu, Zhihong Sun
Summary: This study analyzed the fermentation capacity and metabolic profiles of 17 L. lactis subsp. lactis strains and found significant metabolic differences between strains with different fermentation rates. Peptides, esters, and tributyrin were identified as biomarkers to distinguish between fast and slow fermentation groups.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Microbiology
Zhaoyong Ba, Yujin Lee, Huicui Meng, Penny M. Kris-Etherton, Connie J. Rogers, Zachery T. Lewis, David A. Mills, Emily J. Furumoto, M. Laura Rolon, Jennifer A. Fleming, Robert F. Roberts
Summary: This study compared the effects of delivering Bifidobacterium animas subsp. lactis BB-12 through a yogurt smoothie or a capsule on healthy adults. The results showed that daily consumption of BB-12 did not significantly alter the composition of the gut microbiota, gut transit times, or fecal SCFA concentration in the study cohort.
Article
Critical Care Medicine
Sabina Illi, Martin Depner, Petra Ina Pfefferle, Harald Renz, Caroline Roduit, Diana Hazard Taft, Karen M. Kalanetra, David A. Mills, Freda M. Farquharson, Petra Louis, Elisabeth Schmausser-Hechfellner, Amandine Divaret-Chauveau, Roger Lauener, Anne M. Karvonen, Juha Pekkanen, Pirkka Kirjavainen, Marjut Roponen, Josef Riedler, Michael Kabesch, Bianca Schaub, Erika von Mutius
Summary: This study aimed to assess the association between early life innate immunity and the development of asthma in children at risk. The results showed that within the 17q21 genotype, activated immune responses after innate stimulation can mitigate asthma risk, and this is partly mediated by the gut microbiome.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Guy Shani, Jennifer L. Hoeflinger, Britta E. Heiss, Chad F. Masarweh, Jules A. Larke, Nick M. Jensen, Saumya Wickramasinghe, Jasmine C. Davis, Elisha Goonatilleke, Amr El-Hawiet, Linh Nguyen, John S. Klassen, Carolyn M. Slupsky, Carlito B. Lebrilla, David A. Mills
Summary: This study identifies key gene differences among Bifidobacterium pseudocatenulatum isolates that may impact whether a microbe successfully colonizes an infant gut. The presence or absence of specific alpha-fucosidases seems to direct the strain-specific fucosylated HMO utilization pattern among bifidobacteria. Such knowledge furthers our understanding of how diet drives bacterial colonization of the infant gut.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Nutrition & Dietetics
Anita Vinjamuri, Jasmine C. C. Davis, Sarah M. Totten, Lauren D. Wu, Laura D. Klein, Melanie Martin, E. A. Quinn, Brooke Scelza, Alicia Breakey, Michael Gurven, Grazyna Jasienska, Hillard Kaplan, Claudia Valeggia, Katie Hinde, Jennifer T. Smilowitz, Robin M. Bernstein, Angela M. Zivkovic, Michael J. Barratt, Jeffrey Gordon, Mark A. Underwood, David A. Mills, J. Bruce German, Carlito B. Lebrilla
Summary: This study presents a comprehensive analysis of human milk oligosaccharides (HMOs) in over 1000 mothers from different geographical locations. The results reveal the general behavior of HMOs during lactation and the compositional differences between populations.
JOURNAL OF NUTRITION
(2022)
Article
Nutrition & Dietetics
Karina Cernioglo, Karen M. Kalanetra, Anna Meier, Zachery T. Lewis, Mark A. Underwood, David A. Mills, Jennifer T. Smilowitz
Summary: The supplementation of a probiotic cocktail containing Streptococcus salivarius(K12) for two weeks significantly increased levels of salivary Streptococcus salivarius(K12) when compared to the placebo group. However, the overall oral microbiome was not influenced by time or supplementation.
Meeting Abstract
Biochemistry & Molecular Biology
Jungjae Park, Yapa Wickramasinghe, Karen Kalanetra, David A. Mills, Peng Ji
Article
Microbiology
Andrew Oliver, Zhengyao Xue, Yirui T. Villanueva, Blythe Durbin-Johnson, Zeynep Alkan, Diana H. Taft, Jinxin Liu, Ian Korf, Kevin D. Laugero, Charles B. Stephensen, David A. Mills, Mary E. Kable, Danielle G. Lemay
Summary: Antimicrobial resistance (AMR) is a significant global health problem, and it is predicted to worsen in the future. The microbiome carries antibiotic resistance, and interventions aimed at modifying the gut microbiome may help reduce antibiotic resistance genes (ARGs). This study examined the association between diet and AMR in healthy adults. It found that aminoglycosides were the most prevalent mechanism of AMR, and individuals with low levels of ARGs consumed more fiber in their diets, which was associated with increased abundances of obligate anaerobes in their gut microbiota. Machine learning analysis also revealed that a diverse diet was associated with lower levels of ARGs. These findings suggest that diet could be a potential method for reducing the burden of AMR.
Article
Nutrition & Dietetics
Diana H. Taft, Zachery T. Lewis, Nhu Nguyen, Steve Ho, Chad Masarweh, Vanessa Dunne-Castagna, Daniel J. Tancredi, M. Nazmul Huda, Charles B. Stephensen, Katie Hinde, Erika von Mutius, Pirkka Kirjavainen, Jean-Charles Dalphin, Roger Lauener, Josef Riedler, Jennifer T. Smilowitz, J. Bruce German, Ardythe L. Morrow, David A. Mills
Summary: Bifidobacterium colonization patterns in breastfed infants are related to a country's history of breastfeeding. This study emphasizes the importance of considering historical and cultural influences on the prevalence of gut commensals and understanding bacteria transmission patterns.
Article
Nutrition & Dietetics
Juan J. Castillo, Garret Couture, Nikita P. Bacalzo, Ye Chen, Elizabeth L. Chin, Sarah E. Blecksmith, Yasmine Y. Bouzid, Yael Vainberg, Chad Masarweh, Qingwen Zhou, Jennifer T. Smilowitz, J. Bruce German, David A. Mills, Danielle G. Lemay, Carlito B. Lebrilla
Summary: The molecular complexity of carbohydrates consumed by humans has been oversimplified due to the lack of suitable analytical methods. This work presents a detailed catalogue of glycans in commonly consumed foods and establishes an open-access database. The Glycopedia can be used to formulate targeted diets that modulate the gut microbiome, opening possibilities for new preventative or therapeutic diets.
Article
Gastroenterology & Hepatology
Jules A. Larke, Kara Kuhn-Riordon, Diana H. Taft, Kristin Sohn, Sameeia Iqbal, Mark A. Underwood, David A. Mills, Carolyn M. Slupsky
Summary: This study compares the impact of two probiotic supplements on fecal microbiota and metabolites, as well as gut inflammation in human milk-fed preterm infants. The results demonstrate that supplementing with a HMO-catabolizing Bifidobacterium probiotic increases microbial metabolism of milk oligosaccharides and reduces intestinal inflammation, while a noncatabolizing Lactobacillus probiotic does not have the same effects.
JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION
(2022)
Article
Obstetrics & Gynecology
Kannikar Vongbhavit, Lauren K. Salinero, Karen M. Kalanetra, Chad Masarweh, Alice Yu, Diana H. Taft, David A. Mills, Mark A. Underwood
Summary: Microbial colonization in orogastric and nasogastric tubes show significant differences, with the route of insertion potentially having a greater impact on bacterial populations.
JOURNAL OF PERINATOLOGY
(2022)
Review
Nutrition & Dietetics
J. Bruce German, Carlito Lebrilla, David A. Mills
Summary: The origin, composition, structures, and functions of lactation and milk's biopolymers are important evidence of the Darwinian pressure and selection on lactation as a complete and protective diet. Lactation serves as a sustainable bioreactor with diverse biopolymers that interact with the infant's digestive system from the mammary gland. The interaction between glycan structures in milk and bacteria in the infant's gut has significant health benefits.
FRONTIERS IN NUTRITION
(2022)
Article
Nutrition & Dietetics
Valeria Melendez Hebib, Diana H. Taft, Barbara Stoll, Jinxin Liu, Lee Call, Gregory Guthrie, Nick Jensen, Amy B. Hair, David A. Mills, Douglas G. Burrin
Summary: Necrotizing enterocolitis (NEC) is the leading cause of death caused by gastrointestinal disease in preterm infants. Major risk factors include prematurity, formula feeding, and gut microbial colonization. Probiotics have been shown to reduce NEC incidence in infants, but their effectiveness depends on the specific species used.
Article
Gastroenterology & Hepatology
David A. Mills, J. Bruce German, Carlito B. Lebrilla, Mark A. Underwood
Summary: For more than 100 years, doctors have observed the presence of bifidobacteria in the feces of breast-fed infants, which has been linked to their health. Recent advancements in genomics and glycomics have helped explain this enrichment and allowed for the targeted use of probiotics to restore bifidobacterial functions in at-risk infants. This review highlights two decades of research that has paved the way for the use of bifidobacteria in the intestines of at-risk newborns, and proposes a model for measuring probiotic efficacy in improving infant health based on metabolic outcomes.
Article
Gastroenterology & Hepatology
Britta E. Heiss, Amy M. Ehrlich, Maria X. Maldonado-Gomez, Diana H. Taft, Jules A. Larke, Michael L. Goodson, Carolyn M. Slupsky, Daniel J. Tancredi, Helen E. Raybould, David A. Mills
Summary: The interaction between bacterial-milk glycans alone drives enrichment of beneficial Bifidobacterium, impacting gut microbiota composition, activating anti-inflammatory pathways, and providing protection against chemically-induced colitis. This study demonstrates the importance of human milk oligosaccharides in the colonization of Bifidobacterium in the gut, highlighting the mechanisms of health promotion by bifidobacteria in neonates.
