Michael J. Morowitz
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View article: Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury
Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury Open
Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeut…
View article: Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i>
Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i> Open
Summary Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in lengt…
View article: Plant based enteral nutrition outperforms artificial nutrition in mitigating consequences of antibiotic-induced dysbiosis in mice and humans
Plant based enteral nutrition outperforms artificial nutrition in mitigating consequences of antibiotic-induced dysbiosis in mice and humans Open
Summary Malnutrition, gut inflammation, and antibiotic induced dysbiosis (AID) are omnipresent risk factors for poor clinical outcomes among critically ill patients. We previously showed that commercially available plant-based enteral nutr…
View article: Correction: The salivary microbiota of patients with acute lower respiratory tract infection–A multicenter cohort study
Correction: The salivary microbiota of patients with acute lower respiratory tract infection–A multicenter cohort study Open
[This corrects the article DOI: 10.1371/journal.pone.0290062.].
View article: Crosstalk between DNA Damage Repair and Metabolic Regulation in Hematopoietic Stem Cells
Crosstalk between DNA Damage Repair and Metabolic Regulation in Hematopoietic Stem Cells Open
Self-renewal and differentiation are two characteristics of hematopoietic stem cells (HSCs). Under steady physiological conditions, most primitive HSCs remain quiescent in the bone marrow (BM). They respond to different stimuli to refresh …
View article: The salivary microbiota of patients with acute lower respiratory tract infection–A multicenter cohort study
The salivary microbiota of patients with acute lower respiratory tract infection–A multicenter cohort study Open
The human microbiome contributes to health and disease, but the oral microbiota is understudied relative to the gut microbiota. The salivary microbiota is easily accessible, underexplored, and may provide insight into response to infection…
View article: Neonatal Diet Type and Associations With Adverse Feeding Outcomes in Neonates With Critical Congenital Heart Defects
Neonatal Diet Type and Associations With Adverse Feeding Outcomes in Neonates With Critical Congenital Heart Defects Open
Background: Neonates with critical congenital heart defects (CCHD neonates) experience high rates of feeding intolerance, necrotizing enterocolitis (NEC), and malnutrition. The benefits of human milk and direct chest/breastfeeding are well…
View article: Infant gut DNA bacteriophage strain persistence during the first 3 years of life
Infant gut DNA bacteriophage strain persistence during the first 3 years of life Open
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succ…
View article: Epithelial NAD+ depletion drives mitochondrial dysfunction and contributes to intestinal inflammation
Epithelial NAD+ depletion drives mitochondrial dysfunction and contributes to intestinal inflammation Open
Introduction We have previously demonstrated that a pathologic downregulation of peroxisome proliferator-activated receptor–gamma coactivator 1-alpha (PGC1α) within the intestinal epithelium contributes to the pathogenesis of inflammatory …
View article: Infant gut bacteriophage strain persistence during the first three years of life
Infant gut bacteriophage strain persistence during the first three years of life Open
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we established a large phage sequence database and used strain-resolved analyses to investigate phage succe…
View article: Using strain-resolved analysis to identify contamination in metagenomics data
Using strain-resolved analysis to identify contamination in metagenomics data Open
Background Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study it…
View article: Early antibiotics and risk for necrotizing enterocolitis in premature infants: A narrative review
Early antibiotics and risk for necrotizing enterocolitis in premature infants: A narrative review Open
While prompt initiation of antibiotics at birth due to concerns for early onset sepsis is common, it often leads to many preterm infants being exposed to treatment despite negative blood cultures. Such exposure to early antibiotics can imp…
View article: Additional file 3 of Using strain-resolved analysis to identify contamination in metagenomics data
Additional file 3 of Using strain-resolved analysis to identify contamination in metagenomics data Open
Additional file 3: Table S1. The original and the re-extracted DNA concentrations of four cross-contaminated samples from case study I. *: The re-extracted stool sample (#63D6) is not the same as the original one (#63D9) as the original st…
View article: Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome
Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome Open
The human gut microbiome, which develops and stabilizes during the early stages of infant life, plays an essential role in host health through the production of metabolic resources and the stimulation and training of the immune system. To …
View article: Early Empiric Antibiotic Treatment Among Neonates With Congenital Heart Defects: A Brief Report of an Integrative Review
Early Empiric Antibiotic Treatment Among Neonates With Congenital Heart Defects: A Brief Report of an Integrative Review Open
OBJECTIVES: Despite improved rates of survival, neonates with congenital heart defects experience serious comorbidities. Antibiotics are used widely in other critically ill neonates, and exposure in the first 7 days after birth (early empi…
View article: Using strain-resolved analysis to identify contamination in metagenomics data
Using strain-resolved analysis to identify contamination in metagenomics data Open
Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remain…
View article: Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q
Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q Open
Metagenomic findings suggesting that bacteriophages (phages) can use genetic codes different from those of their host bacteria reveal a new dimension of phage-host interaction dynamics. Whereas reassignment of stop codons to code for amino…
View article: Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition
Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition Open
Gut microbiome succession affects infant development. However, it remains unclear what factors promote persistence of initial bacterial colonizers in the developing gut. Here, we perform strain-resolved analyses to compare gut colonization…
View article: Sustained Dysbiosis and Decreased Fecal Short-Chain Fatty Acids after Traumatic Brain Injury and Impact on Neurologic Outcome
Sustained Dysbiosis and Decreased Fecal Short-Chain Fatty Acids after Traumatic Brain Injury and Impact on Neurologic Outcome Open
Traumatic brain injury (TBI) alters microbial populations present in the gut, which may impact healing and tissue recovery. However, the duration and impact of these changes on outcome from TBI are unknown. Short-chain fatty acids (SCFAs),…
View article: Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition
Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition Open
SUMMARY Gut microbiome succession impacts infant development. However, it remains unclear what factors promote persistence of initial bacterial colonists in the developing gut. Here, we performed strain-resolved metagenomic analyses to com…
View article: Dynamics of the preterm gut microbiome in health and disease
Dynamics of the preterm gut microbiome in health and disease Open
Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in t…
View article: Additional file 11 of Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics
Additional file 11 of Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics Open
Additional file 10.