@article {pmid30659855,
year = {2019},
author = {Huh, H and Wong, S and St Jean, J and Slavcev, R},
title = {Bacteriophage Interactions with Mammalian Tissue: Therapeutic Applications.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.addr.2019.01.003},
pmid = {30659855},
issn = {1872-8294},
abstract = {The human body is a large reservoir for bacterial viruses known as bacteriophages (phages), which participate in dynamic interactions with their bacterial and human hosts that ultimately affect human health. The current growing interest in human resident phages is paralleled by new uses of phages, including the design of engineered phages for therapeutic applications. Despite the increasing number of clinical trials being conducted, the understanding of the interaction of phages and mammalian cells and tissues is still largely unknown. The presence of phages in compartments within the body previously considered purely sterile, suggests that phages possess a unique capability of bypassing anatomical and physiological barriers characterized by varying degrees of selectivity and permeability. This review will discuss the direct evidence of the accumulation of bacteriophages in various tissues, focusing on the unique capability of phages to traverse relatively impermeable barriers in mammals and its relevance to its current applications in therapy.},
}

@article {pmid30659564,
year = {2018},
author = {Gulas, E and Wysiadecki, G and Strzelecki, D and Gawlik-Kotelnicka, O and Polguj, M},
title = {Can microbiology affect psychiatry? A link between gut microbiota and psychiatric disorders.},
journal = {Psychiatria polska},
volume = {52},
number = {6},
pages = {1023-1039},
doi = {10.12740/PP/OnlineFirst/81103},
pmid = {30659564},
issn = {2391-5854},
abstract = {Every single human consists of thousands of genes, billions of neurons and trillions of bacteria. There is a rapidly growing number of data that links the gut microbiome to the development and functioning of the central nervous system, which is a currently proposed paradigm shift in neuroscience. Knowledge on the relationship between gut microbiota and mental disorders is constantly increasing. This phenomenon is known as "gut-brain axis". The strongest evidence for the role of microbes in the gut-brain axis comes from animal studies. Nevertheless, the gutbrain crosstalk is a bidirectional communication system that not only provides gastrointestinal homeostasis, but can also affect motivation as well as higher cognitive functions. Moreover, gut microbiome can be associated with obesity and inflammatory gastrointestinal disorders. According to the recent studies, there is a link between the composition of gut microbiota and mental disorders in animals (response to depression and chronic stress). This subject requires further examination, especially taking into consideration potential therapeutic options.},
}

@article {pmid30659556,
year = {2019},
author = {Del Campo, R and Martínez-García, L and Sánchez-Díaz, AM and Baquero, F},
title = {Biology of Hand-to-Hand Bacterial Transmission.},
journal = {Microbiology spectrum},
volume = {7},
number = {1},
pages = {},
doi = {10.1128/microbiolspec.MTBP-0011-2016},
pmid = {30659556},
issn = {2165-0497},
abstract = {Numerous studies have demonstrated that adequate hand hygiene among hospital staff is the best measure to prevent hand-to-hand bacterial transmission. The skin microbiome is conditioned by the individual physiological characteristics and anatomical microenvironments. Furthermore, it is important to separate the autochthonous resident microbiota from the transitory microbiota that we can acquire after interactions with contaminated surfaces. Two players participate in the hand-to-hand bacterial transmission process: the bacteria and the person. The particularities of the bacteria have been extensively studied, identifying some genera or species with higher transmission efficiency, particularly those linked to nosocomial infections and outbreaks. However, the human factor remains unstudied, and intrapersonal particularities in bacterial transmission have not been yet explored. Herein we summarize the current knowledge on hand-to-hand bacterial transmission, as well as unpublished results regarding interindividual and interindividual transmission efficiency differences. We designed a simple in vivo test based on four sequential steps of finger-to-finger contact in the same person artificially inoculated with a precise bacterial inoculum. Individuals can be grouped into one of three observed transmission categories: high, medium, and poor finger-to-finger transmitters. Categorization is relevant to predicting the ultimate success of a human transmission chain, particularly for the poor transmitters, who have the ability to cut the transmission chain. Our model allowed us to analyze transmission rate differences among five bacterial species and clones that cause nosocomial infections, from which we detected that Gram-positive microorganisms were more successfully transmitted than Gram-negative.},
}

@article {pmid30659375,
year = {2019},
author = {Weinberg, BA and Marshall, JL},
title = {Colon Cancer in Young Adults: Trends and Their Implications.},
journal = {Current oncology reports},
volume = {21},
number = {1},
pages = {3},
doi = {10.1007/s11912-019-0756-8},
pmid = {30659375},
issn = {1534-6269},
abstract = {PURPOSE OF REVIEW: The recent rise of young individuals under age 50 with colorectal cancer (CRC) is a startling trend in need of greater focus and research. The etiology of young-onset CRC is unexplained as efforts to blame obesity or diabetes as causative factors are simplistic and inadequate.

RECENT FINDINGS: We describe the epidemiologic shifts of CRC incidence and mortality across age groups as well as the differences in clinicopathologic, molecular, treatment, and survival characteristics between young and older patients. Novel studies of the microbiome may elucidate bacterial causes of CRC carcinogenesis in younger individuals. Moving up the colonoscopy screening to age 45 in normal-risk individuals should prove beneficial in detecting more patients with early-onset CRC. We favor the development of risk-adaptive screening decision algorithms and flexible sigmoidoscopy screening at age 40 given the predilection for left-sided primaries in this age group. More awareness and attention to young-onset CRC will be critical to improve outcomes in this patient population.},
}

@article {pmid30659231,
year = {2019},
author = {Bruesch, I and Meier, P and Vital, M and Pieper, DH and Selke, K and Böhlen, S and Basic, M and Meier, M and Glage, S and Hundrieser, J and Wedekind, D and Buettner, M and Bleich, A},
title = {Analysis of Cdcs1 colitogenic effects in the hematopoietic compartment reveals distinct microbiome interaction and a new subcongenic interval active in T cells.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41385-019-0133-9},
pmid = {30659231},
issn = {1935-3456},
abstract = {Disease activity in Interleukin-10-deficient (Il10-/-) mice, a model for IBD, depends on genetic background and microbiome composition. B6.129P2/JZtm-Il10tm1Cgn (B6-Il10-/-) mice are partially resistant to colitis, whereas mice carrying the Cdcs1C3Bir haplotype on chromosome 3, B6.Cg-Il10tm1CgnMMU3(D3Mit11-D3Mit348)/JZtm (BC-R3-Il10-/-), are susceptible. This study was performed to clarify Cdcs1 and candidate gene effects on the colitogenic potential of hematopoietic cells using bone marrow (BM) and T-cell transfer models. Acute and chronic graft versus host reaction was excluded by high-density genotyping, in vitro and in vivo approaches. BM-chimeras were created with animals housed in two barriers (I and II) with distinct microbiota composition as identified by sequencing. BM-chimeras of all groups developed comparable moderate-to-severe colitis in Barrier I, however, in Barrier II only recipients of BC-R3-Il10-/- BM. Subsequent adoptive T cell transfers pointed to a new subcongenic interval within Cdcs1 affecting their colitogenic potential. Transfers excluded Larp7 and Alpk1 but highlighted Ifi44 as potential candidate genes. In this model-system, colitis development after cell transfer heavily depends on microbiome, though Cdcs1 acts mainly independently in hematopoietic cells. A new subcongenic interval, provisionally named Cdcs1.4, modifies colitogenic T cell function. Within this locus, Ifi44 represents an important candidate gene for colitis expression.},
}

@article {pmid30659041,
year = {2019},
author = {Costiniuk, CT and Saneei, Z and Routy, JP and Margolese, S and Mandarino, E and Singer, J and Lebouché, B and Cox, J and Szabo, J and Brouillette, MJ and Klein, MB and Chomont, N and Jenabian, MA},
title = {Oral cannabinoids in people living with HIV on effective antiretroviral therapy: CTN PT028-study protocol for a pilot randomised trial to assess safety, tolerability and effect on immune activation.},
journal = {BMJ open},
volume = {9},
number = {1},
pages = {e024793},
doi = {10.1136/bmjopen-2018-024793},
pmid = {30659041},
issn = {2044-6055},
abstract = {INTRODUCTION: Despite antiretroviral therapy (ART), people living with HIV have higher rates of non-infectious chronic diseases. These conditions are driven by relatively high levels of inflammation persisting on ART compared with uninfected individuals. Chronic inflammation also contributes to HIV persistence during ART. Cannabis when taken orally may represent a way to reduce inflammation and strengthen immune responses. Before planning large interventional studies, it is important to ensure that cannabis taken orally is safe and well tolerated in people living with HIV. We propose to conduct a pilot randomised trial to examine the safety and tolerability of cannabis oils containing tetrahydrocannabinol (THC) and cannabidiol (CBD) consumed orally in people living with HIV. We will also measure inflammatory markers, markers of HIV persistence in peripheral blood cells and changes in the gastrointestinal microbiome.

METHODS AND ANALYSIS: Twenty-six people living with HIV having undetectable viral load for at least 3 years will be randomised to receive TN-TC11LM (THC:CBD in 1:1 ratio) or TN-TC19LM (THC:CBD in 1:9 ratio) capsules daily for 12 weeks. Safety and tolerability of these capsules will be assessed through haematological, hepatic and renal blood tests, face-to-face interviews and questionnaires. Proportions of participants without any signs of significant toxicity (grades 0-2 scores on the WHO toxicity scale) and who complete the study, as well as scores on quality of life and mood will be examined using descriptive statistics. The effects on inflammatory markers, markers of peripheral blood reservoir size and effect on the composition of the gastrointestinal microbiome will be assessed before and after study completion.

ETHICS AND DISSEMINATION: This study has been approved by the Research Institute of the McGill University Health Centre. A Data Safety Monitor will review safety information at regular intervals. The final manuscript will be submitted to an open-access journal within 6 months of study completion.

TRIAL REGISTRATION NUMBER: NCT03550352.},
}

@article {pmid30659010,
year = {2019},
author = {Bhat, P and Bhaskar, M and Sistla, S and Kadhiravan, T},
title = {Fatal case of necrotising fasciitis due to Vibrio vulnificus in a patient with alcoholic liver disease and diabetes mellitus.},
journal = {BMJ case reports},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bcr-2018-227851},
pmid = {30659010},
issn = {1757-790X},
abstract = {Vibrio vulnificus is a halophilic Vibrio found globally. They are thought to be normal microbiome in the estuaries along the coasts associated with seawater and seashells. Infection usually results from consumption of raw oysters or shellfish or exposure of broken skin or open wounds to contaminated salt or brackish water. Clinical manifestations range from gastroenteritis to skin and subcutaneous infection and primary sepsis. Pathogen has the ability to cause infections with significant mortality in high-risk populations, including patients with chronic liver disease, immunodeficiency, diabetes mellitus and iron storage disorders. There is often a lack of clinical suspicion in cases due to Vibrio vulnificus leading to delay in treatment and subsequent mortality. Herein we report a case of necrotising fasciitis in a diabetic patient with alcoholic liver disease caused by Vibrio vulnificus which ended fatally.},
}

@article {pmid30658995,
year = {2019},
author = {Hildebrand, F and Moitinho-Silva, L and Blasche, S and Jahn, MTT and Gossmann, TI and Heuerta Cepas, J and Hercog, R and Luetge, M and Bahram, M and Pryszlak, A and Alves, RJ and Waszak, SM and Zhu, A and Ye, L and Costea, PI and Aalvink, S and Belzer, C and Forslund, SK and Sunagawa, S and Hentschel, U and Merten, C and Patil, KR and Benes, V and Bork, P},
title = {Antibiotics-induced monodominance of a novel gut bacterial order.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2018-317715},
pmid = {30658995},
issn = {1468-3288},
abstract = {OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.

DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.

RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.

CONCLUSION: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.},
}

@article {pmid30658982,
year = {2019},
author = {Jiao, S and Chen, W and Wei, G},
title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02523-18},
pmid = {30658982},
issn = {1098-5336},
abstract = {Lacking knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of different plant growth were explored via sequencing of the 16S rRNA amplicon and shotgun metagenomics. Soil microbial alpha-diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles compared with functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals strong resilience of soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.Importance Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon-degradation and metal-tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.},
}

@article {pmid30658973,
year = {2019},
author = {Malmuthuge, N and Liang, G and Griebel, PJ and Guan, LL},
title = {Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02534-18},
pmid = {30658973},
issn = {1098-5336},
abstract = {A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole genome sequencing of metagenome, aiming to understand the dynamics of microbial establishment during the early life. Despite highly individualized microbial communities, we identified two distinct taxonomic-based clusters from the collective luminal microbiomes comprising either a high level of Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus-dominant ileal microbiomes had significantly lower abundances of Bacteroides, Prevotella, Roseburia, Ruminococcus, and Veillonella compared to the Bacteroides-dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus-dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides-dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of MAPK cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2±0.1%) compared to the protein metabolism-dominant cluster (12.6±5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium, which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves.Importance Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding on early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to develop dietary interventions to improve calf gut health. The use of metagenome sequencing based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the pre-weaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density and the abundance taxa and functions were observed. A correlation based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.},
}

@article {pmid30658882,
year = {2019},
author = {Israelyan, N and Margolis, KG},
title = {Reprint of: Serotonin as a link between the gut-brain-microbiome axis in autism spectrum disorders.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.phrs.2018.12.023},
pmid = {30658882},
issn = {1096-1186},
abstract = {Autism-spectrum disorder (ASD) is a neurodevelopmental disorder characterized by persistent deficits in social communication and repetitive patterns of behavior. ASD is, however, often associated with medical comorbidities and gastrointestinal (GI) dysfunction is among the most common. Studies have demonstrated a correlation between GI dysfunction and the degree of social impairment in ASD. The etiology of GI abnormalities in ASD is unclear, though the association between GI dysfunction and ASD-associated behaviors suggest that overlapping developmental defects in the brain and the intestine and/or a defect in communication between the enteric and central nervous systems (ENS and CNS, respectively), known as the gut-brain axis, could be responsible for the observed phenotypes. Brain-gut abnormalities have been increasingly implicated in several disease processes, including ASD. As a critical modulator of ENS and CNS development and function, serotonin may be a nexus for the gut-brain axis in ASD. This paper reviews the role of serotonin in ASD from the perspective of the ENS. A murine model that has been demonstrated to possess brain, behavioral and GI abnormalities mimicking those seen in ASD harbors the most common serotonin transporter (SERT) based mutation (SERT Ala56) found in children with ASD. Discussion of the gut-brain manifestations in the SERT Ala56 mice, and their correction with developmental administration of a 5-HT4 agonist, are also addressed in conjunction with other future directions for diagnosis and treatment.},
}

@article {pmid30658727,
year = {2019},
author = {Sarin, SK and Pande, A and Schnabl, B},
title = {Microbiome as a therapeutic target in alcohol-related liver disease.},
journal = {Journal of hepatology},
volume = {70},
number = {2},
pages = {260-272},
doi = {10.1016/j.jhep.2018.10.019},
pmid = {30658727},
issn = {1600-0641},
abstract = {Alcohol-related liver disease is associated with significant changes in gut microbial composition. The transmissibility of ethanol-induced liver disease has been demonstrated using faecal microbiota transfer in preclinical models. This technique has also led to improved survival in patients with severe alcoholic hepatitis, suggesting that changes in the composition and function of the gut microbiota are causatively linked to alcohol-related liver disease. A major mechanism by which gut microbiota influence the development of alcohol-related liver disease is through a leaky intestinal barrier. This permits translocation of viable bacteria and microbial products to the liver, where they induce and promote inflammation, as well as contribute to hepatocyte death and the fibrotic response. In addition, gut dysbiosis is associated with changes in the metabolic function of the intestinal microbiota, bile acid composition and circulation, immune dysregulation during onset and progression of alcohol-related liver disease. Findings from preclinical and human studies will be used to demonstrate how alcohol causes intestinal pathology and contributes to alcohol-related liver disease and how the latter is self-perpetuating. Additionally, we summarise the effects of untargeted treatment approaches on the gut microbiota, such as diet, probiotics, antibiotics and faecal microbial transplantation in alcohol-related liver disease. We further discuss how targeted approaches can restore intestinal homeostasis and improve alcohol-related liver disease. These approaches are likely to add to the therapeutic options for alcohol-related liver disease independently or in conjunction with steroids.},
}

@article {pmid30658700,
year = {2019},
author = {Heras, VL and Clooney, AG and Ryan, FJ and Cabrera-Rubio, R and Casey, PG and Hueston, CM and Pinheiro, J and Rudkin, JK and Melgar, S and Cotter, PD and Hill, C and Gahan, CGM},
title = {Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {7},
doi = {10.1186/s40168-019-0621-x},
pmid = {30658700},
issn = {2049-2618},
support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 641984//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {BACKGROUND: A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the implications of such diets for the progression of infectious disease. Here, we investigated the influence of a high-fat (HF) diet upon parameters that influence Listeria monocytogenes infection in mice.

RESULTS: We determined that short-term administration of a HF diet increases the number of goblet cells, a known binding site for the pathogen, in the gut and also induces profound changes to the microbiota and promotes a pro-inflammatory gene expression profile in the host. Host physiological changes were concordant with significantly increased susceptibility to oral L. monocytogenes infection in mice fed a HF diet relative to low fat (LF)- or chow-fed animals. Prior to Listeria infection, short-term consumption of HF diet elevated levels of Firmicutes including Coprococcus, Butyricicoccus, Turicibacter and Clostridium XIVa species. During active infection with L. monocytogenes, microbiota changes were further exaggerated but host inflammatory responses were significantly downregulated relative to Listeria-infected LF- or chow-fed groups, suggestive of a profound tempering of the host response influenced by infection in the context of a HF diet. The effects of diet were seen beyond the gut, as a HF diet also increased the sensitivity of mice to systemic infection and altered gene expression profiles in the liver.

CONCLUSIONS: We adopted a systems approach to identify the effects of HF diet upon L. monocytogenes infection through analysis of host responses and microbiota changes (both pre- and post-infection). Overall, the results indicate that short-term consumption of a westernized diet has the capacity to significantly alter host susceptibility to L. monocytogenes infection concomitant with changes to the host physiological landscape. The findings suggest that diet should be a consideration when developing models that reflect human infectious disease.},
}

@article {pmid30658591,
year = {2019},
author = {Horsley, A and Thaler, DS},
title = {Microwave detection and quantification of water hidden in and on building materials: implications for healthy buildings and microbiome studies.},
journal = {BMC infectious diseases},
volume = {19},
number = {1},
pages = {67},
doi = {10.1186/s12879-019-3720-1},
pmid = {30658591},
issn = {1471-2334},
abstract = {BACKGROUND: Excess water in all its forms (moisture, dampness, hidden water) in buildings negatively impacts occupant health but is hard to reliably detect and quantify. Recent advances in through-wall imaging recommend microwaves as a tool with a high potential to noninvasively detect and quantify water throughout buildings.

METHODS: Microwaves in both transmission and reflection (radar) modes were used to perform a simple demonstration of the detection of water both on and hidden within building materials.

RESULTS: We used both transmission and reflection modes to detect as little as 1 mL of water between two 7 cm thicknesses of concrete. The reflection mode was also used to detect 1 mL of water on a metal surface. We observed oscillations in transmitted and reflected microwave amplitude as a function of microwave wavelength and water layer thickness, which we attribute to thin-film interference effects.

CONCLUSIONS: Improving the detection of water in buildings could help design, maintenance, and remediation become more efficient and effective and perhaps increase the value of microbiome sequence data. Microwave characterization of all forms of water throughout buildings is possible; its practical development would require new collaborations among microwave physicists or engineers, architects, building engineers, remediation practitioners, epidemiologists, and microbiologists.},
}

@article {pmid30658587,
year = {2019},
author = {Dalman, M and Bhatta, S and Nagajothi, N and Thapaliya, D and Olson, H and Naimi, HM and Smith, TC},
title = {Characterizing the molecular epidemiology of Staphylococcus aureus across and within fitness facility types.},
journal = {BMC infectious diseases},
volume = {19},
number = {1},
pages = {69},
doi = {10.1186/s12879-019-3699-7},
pmid = {30658587},
issn = {1471-2334},
abstract = {BACKGROUND: Staphylococcus aureus is a common bacterium found in the nose and throat of healthy individuals, and presents risk factors for infection and death. We investigated environmental contamination of fitness facilities with S. aureus in order to determine molecular types and antibiotic susceptibility profiles of contaminates that may be transmitted to facility patrons.

METHODS: Environmental swabs (n = 288) were obtained from several fitness facilities (n = 16) across Northeast Ohio including cross-fit type facilities (n = 4), traditional iron gyms (n = 4), community center-based facilities (n = 5), and hospital-associated facilities (n = 3). Samples were taken from 18 different surfaces at each facility and were processed within 24 h using typical bacteriological methods. Positive isolates were subjected to antibiotic susceptibility testing and molecular characterization (PVL and mecA PCR, and spa typing).

RESULTS: The overall prevalence of S. aureus on environmental surfaces in the fitness facilities was 38.2% (110/288). The most commonly colonized surfaces were the weight ball (62.5%), cable driven curl bar, and CrossFit box (62.5%), as well as the weight plates (56.3%) and treadmill handle (50%). Interestingly, the bathroom levers and door handles were the least contaminated surfaces in both male and female restroom facilities (18.8%). Community gyms (40.0%) had the highest contamination prevalence among sampled surfaces with CrossFit (38.9%), traditional gyms (38.9%), and hospital associated (33.3%) contaminated less frequently, though the differences were not significant (p = 0.875). The top spa types found overall were t008 (12.7%), t267 (10.0%), t160, t282, t338 (all at 5.5%), t012 and t442 (4.5%), and t002 (3.6%). t008 and t002 was found in all fitness facility types accept Crossfit, with t267 (25%), t548, t377, t189 (all 10.7%) the top spa types found within crossfit. All samples were resistant to benzylpenicillin, with community centers having significantly more strains resistant to oxacillin (52.8%), erythromycin (47%), clindamycin (36%), and ciprofloxacin (19%). Overall, 36.3% of isolates were multidrug resistant.

CONCLUSIONS: Our pilot study indicates that all facility types were contaminated by S. aureus and MRSA, and that additional studies are needed to characterize the microbiome structure of surfaces at different fitness facility types and the patrons at these facilities.},
}

@article {pmid30658055,
year = {2019},
author = {Pellock, SJ and Walton, WG and Ervin, SM and Torres-Rivera, D and Creekmore, BC and Bergan, G and Dunn, ZD and Li, B and Tripathy, A and Redinbo, MR},
title = {Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmb.2019.01.013},
pmid = {30658055},
issn = {1089-8638},
abstract = {The human gut microbiota encodes β-glucuronidases (GUS) that play key roles in health and disease via the metabolism of glucuronate-containing carbohydrates and drugs. Hundreds of putative bacterial GUS enzymes have been identified by metagenomic analysis of the human gut microbiome, but less than 10% have characterized structures and functions. Here we describe a set of unique gut microbial GUS enzymes that bind flavin mononucleotide (FMN). First, we show using mass spectrometry, isothermal titration calorimetry, and x-ray crystallography that a purified GUS from the gut commensal microbe Faecalibacterium prausnitzii binds to FMN on a surface groove located 30 Å away from the active site. Second, utilizing structural and functional data from this FMN-binding GUS, we analyzed the 279 unique GUS sequences from the human microbiome project database and identified 14 putative FMN-binding GUSs. We characterized four of these hits and solved the structure of two, the GUSs from Ruminococcus gnavus and Roseburia hominis, which confirmed that these are FMN binders. Third, binding and kinetic analysis of the FMN-binding site mutants of these five GUSs show that they utilize a conserved site to bind FMN that is not essential for GUS activity, but can affect KM. Lastly, a comprehensive structural review of the PDB reveals that the FMN-binding site employed by these enzymes is unlike any structurally characterized FMN-binders to date. These findings reveal the first instance of an FMN-binding glycoside hydrolase and suggest a potential link between FMN and carbohydrate metabolism in the human gut microbiota.},
}

@article {pmid30657624,
year = {2019},
author = {Gazdeck, KR and Fruscione, SR and Adami, GR and Zhou, Y and Cooper, LF and Schwartz, JL},
title = {Diversity of the Oral Microbiome Between Dentate and Edentulous Individuals.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.13039},
pmid = {30657624},
issn = {1601-0825},
abstract = {BACKGROUND: Measurement of saliva microbes is promoted as a way to detect oral and systemic disease, yet there is a multitude of factors that affect the oral microbiome. The salivary microbiome is influenced by oral biofilm of shedding (epithelial) and non-shedding (tooth) surfaces.

METHODS: To gauge the ability of salivary microbial analytics to distinguish between edentulous and dentate oral conditions, we looked for differences in the saliva microbiome of subjects with and without teeth. 52 dentate and 49 edentulous subjects provided stimulated saliva samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analysis was done using several different analytical approaches to detect differences in the salivary microbiome between the two groups.

RESULTS: Bacteria diversity was lower in the edentulous group. Remarkably, all 31 of the most significant differences in taxa were deficits that occur in the edentulous group. As one might expect many of these taxa are attributed to dental plaque and gingival sulcus associated bacteria.

CONCLUSION: In sum, the measurement of 16S rRNA genes in the bacteria of the saliva can be used to reproducibly measure differences in the oral microbiome that occur with edentulism, mainly the lack of tooth and tooth related structures. This article is protected by copyright. All rights reserved.},
}

@article {pmid30657195,
year = {2019},
author = {Espin-Garcia, O and Croitoru, K and Xu, W},
title = {A finite mixture model for X-chromosome association with an emphasis on microbiome data analysis.},
journal = {Genetic epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/gepi.22190},
pmid = {30657195},
issn = {1098-2272},
support = {RGPIN-2017-06672//Natural Sciences and Engineering Research Council of Canada/ ; 145546//Canadian Institutes of Health Research/Canada ; GET-101831//Canadian Institutes of Health Research/Canada ; CMF108031//Canadian Institutes of Health Research/Canada ; //Crohn's and Colitis Canada Grant CCC-GEMIII/ ; //Helmsley Charitable Trust/ ; },
abstract = {Analysis of the X chromosome has been largely neglected in genetic studies mainly because of complex underlying biological mechanisms. On the other hand, the study of human microbiome data (typically over-dispersed counts with an excess of zeros) has generated great interest recently because of advancements in next-generation sequencing technologies. We propose a novel approach to infer the association between host genetic variants in the X-chromosome and microbiome data. The method accounts for random X-chromosome inactivation (XCI), skewed (or nonrandom) XCI (XCI-S), and escape of XCI (XCI-E). The inference is performed through a finite mixture model (FMM), in which an indicator variable denoting the "true" biological mechanism is treated as missing data. An expectation-maximization algorithm on zero-inflated and two-part models is implemented to estimate genetic effects. We investigate the performance of the FMM along with strategies that assume XCI and XCI-E mechanisms for all subjects compared with alternative approaches. Briefly, an XCI mechanism codes males' genotypes as homozygous females, whereas under XCI-E, males are treated as heterozygous females. By comprehensive simulations, we evaluate tests of the hypothesis under a computationally efficient score statistic. In summary, the FMM renders reduced bias and commensurate power compared to XCI, XCI-E, and alternative strategies while maintaining adequate Type 1 error control. The proposed method has far-reaching applications. In particular, we illustrate its usage on a large-scale human microbiome study, the Genetic, Environmental and Microbial (GEM) project, to test for the genetic association on the X chromosome.},
}

@article {pmid30657007,
year = {2019},
author = {Machiavelli, A and Duarte, RTD and Pires, MMS and Zarate-Bladés, CR and Pinto, AR},
title = {The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/19490976.2018.1560768},
pmid = {30657007},
issn = {1949-0984},
abstract = {HIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.},
}

@article {pmid30656737,
year = {2019},
author = {Ahluwalia, J and Borok, J and Ahluwalia, RS and Schwartz, EW and Hosseini, D and Amini, S and Eichenfield, LF},
title = {The microbiome in preadolescent acne: Assessment and prospective analysis of the influence of benzoyl peroxide.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.13741},
pmid = {30656737},
issn = {1525-1470},
abstract = {BACKGROUND/OBJECTIVES: The pathogenesis of preadolescent acne has not been well studied, and it is uncertain if Cutibacterium acnes is a predominant organism in the microbiome in this age group. The aim of this study was to analyze the microbiome of preadolescent females and to assess whether benzoyl peroxide impacts the microbiome.

METHODS: The study enrolled girls, aged 7-12 years, with evidence of at least six acne lesions who had not been previously treated. Participants' skin surface of forehead, cheeks, nose, chin, left retroauricular crease, and extruded contents of a comedonal lesion were sampled at baseline. Participants used benzoyl peroxide 4% wash for 6-8 weeks and returned for skin surface sampling and extraction collection. Microbiome analysis was performed using 16S ribosomal RNA gene amplicon sequencing on all swab and lesional extraction samples.

RESULTS: Fifty-one participants were enrolled with a median IGA score of 2 (mild). Changes in microbiome diversity were associated with increasing age and number of acne lesions (P = 0.001). C. acnes had higher abundances on forehead and nose, as opposed to cheeks and chin (P = 0.009). Bacterial diversity (alpha diversity) of the skin microbiome was comparable between preadolescent at baseline and after treatment with benzoyl peroxide.

CONCLUSION: This is the first large assessment characterizing female acne microbiome in early and late preadolescence. Results show that preadolescent acne can vary in its microbial profile, reflecting surrounding changes associated with the onset of puberty. Although benzoyl peroxide use was associated with decreased acne counts, its effect on microbial diversity was not demonstrated in our study.},
}

@article {pmid30656588,
year = {2019},
author = {Kwon, MJ and Jung, JY and Tripathi, BM and Göckede, M and Lee, YK and Kim, M},
title = {Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12275-019-8661-2},
pmid = {30656588},
issn = {1976-3794},
abstract = {Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.},
}

@article {pmid30655720,
year = {2019},
author = {Moreno, I and Simon, C},
title = {Deciphering the effect of reproductive tract microbiota on human reproduction.},
journal = {Reproductive medicine and biology},
volume = {18},
number = {1},
pages = {40-50},
doi = {10.1002/rmb2.12249},
pmid = {30655720},
issn = {1445-5781},
abstract = {Background: The female reproductive tract contains an active microbiome comprising mainly bacteria from the Lactobacillus genus, which is associated with a healthy microbiome state. However, spatio-temporal fluctuations of this microbiome that occur in response to internal and external factors may impact the physiology of the reproductive tract organs and even lead to pathological states.

Methods: Current literature covering the reproductive tract microbiome is summarized and contextualized in this review.

Main findings: This review presents the current knowledge about the bacterial composition of the lower and upper reproductive tract as well as the impact of the microbiota on women's health and reproduction. We place special focus on the impact of the endometrial microbiome in infertility and assisted reproductive technologies.

Conclusion: The assessment of the reproductive tract microbiome adds a new microbiological perspective to human reproduction, pregnancy, and onset of new life, highlighting the importance of considering the evaluation of microbial communities to improve personalized care in reproductive medicine and women's health.},
}

@article {pmid30655102,
year = {2019},
author = {Steer, E},
title = {A cross comparison between Ayurvedic etiology of Major Depressive Disorder and bidirectional effect of gut dysregulation.},
journal = {Journal of Ayurveda and integrative medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaim.2017.08.002},
pmid = {30655102},
issn = {0975-9476},
abstract = {Ayurveda, an Indian medical science has been practiced for thousands of years. What makes Ayurveda relevant today is its subtle understanding of the environment and its focus on the generation of good health through one's own lifestyle choices. The digestive system has long been an area of critical importance within the Ayurvedic system and is only now being acknowledged by modern science as a key component in the regulation of physical and mental well-being. The gut microbiome and enteric nervous system are two particular areas in which the onset of psychiatric disorders, such as depression, have been associated. There are some striking similarities between this biomedical understanding of the gastrointestinal system and the Ayurvedic perspective of disease development. Major Depressive Disorder (MDD) is becoming increasingly linked with gut dysregulation in contemporary literature and is a pathology explored within both the Ayurvedic and Western systems of medicine. This literature review seeks to draw parallels between these two areas of study and highlight the importance of the digestive system when diagnosing and treating MDD.},
}

@article {pmid30655087,
year = {2019},
author = {Markowski, MC and Boorjian, SA and Burton, JP and Hahn, NM and Ingersoll, MA and Vareki, SM and Pal, SK and Sfanos, KS},
title = {The Microbiome and Genitourinary Cancer: A Collaborative Review.},
journal = {European urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eururo.2018.12.043},
pmid = {30655087},
issn = {1873-7560},
abstract = {CONTEXT: The recent discovery of the existence of a human genitourinary microbiome has led to the investigation of its role in mediating the pathogenesis of genitourinary malignancies, including bladder, kidney, and prostate cancers. Furthermore, although it is largely recognized that members of the gastrointestinal microbiota are actively involved in drug metabolism, new studies demonstrate additional roles and the potential necessity of the gastrointestinal microbiota in dictating cancer treatment response.

OBJECTIVE: To summarize the current evidence of a mechanistic role for the genitourinary and gastrointestinal microbiome in genitourinary cancer initiation and treatment response.

EVIDENCE ACQUISITION: We conducted a literature search up to October 2018. Search terms included microbiome, microbiota, urinary microbiome, bladder cancer, urothelial carcinoma, renal cell carcinoma, kidney cancer, testicular cancer, and prostate cancer.

EVIDENCE SYNTHESIS: There is preliminary evidence to implicate the members of the genitourinary microbiota as causative factors or cofactors in genitourinary malignancy. Likewise, the current evidence for gastrointestinal microbes in dictating cancer treatment response is mainly correlative; however, we provide examples where therapeutic agents used for the treatment of genitourinary cancers are affected by the human-associated microbiota, or vice versa. Clinical trials, such as fecal microbiota transplant to increase the efficacy of immunotherapy, are currently underway.

CONCLUSIONS: The role of the microbiome in genitourinary cancer is an emerging field that merits further studies. Translating microbiome research into clinical action will require incorporation of microbiome surveillance into ongoing and future clinical trials as well as expansion of studies to include metagenomic sequencing and metabolomics.

PATIENT SUMMARY: This review covers recent evidence that microbial populations that reside in the genitourinary tract-and were previously not known to exist-may influence the development of genitourinary malignancies including bladder, kidney, and prostate cancers. Furthermore, microbial populations that exist at sites outside of the genitourinary tract, such as those that reside in our gut, may influence cancer development and/or treatment response.},
}

@article {pmid30655037,
year = {2019},
author = {Leung, CY and Weitz, JS},
title = {Not by (Good) Microbes Alone: Towards Immunocommensal Therapies.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2018.12.006},
pmid = {30655037},
issn = {1878-4380},
abstract = {Commensal bacteria have been identified as critical drivers of host resilience to pathogen invasion. The resulting 'competitive exclusion' of pathogens by commensals can arise via multiple mechanisms, including direct competition for sites of colonization, production of metabolic products that inhibit pathogen growth, and modulation of host immune responses (including differential targeting of pathogens). Nonetheless, suppression of pathogens through the combined action of commensals and host immunity is far from inevitable. Here, we utilize a simple, within-host ecosystem model to explore the microbiological and immunological conditions that govern the fate of pathogen colonization. Model analysis leads to the hypothesis that robust elimination of pathogens requires a synergy between host immune defense and commensal bacteria. That is, pathogens can proliferate and establish persistent infections if either the state of the microbiota or the host immune defense falls below critical levels. Leveraging these findings, we advocate for improved integration of nonlinear dynamic models in efforts to understand infection dynamics in an immunological context. Doing so may provide new opportunities to establish baseline indicators for healthy microbiomes and to develop improved therapeutics through targeted modification of feedback amongst commensals and between commensals and the immune system.},
}

@article {pmid30654751,
year = {2019},
author = {Vongsa, R and Hoffman, D and Shepard, K and Koenig, D},
title = {Comparative study of vulva and abdominal skin microbiota of healthy females with high and average BMI.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {16},
doi = {10.1186/s12866-019-1391-0},
pmid = {30654751},
issn = {1471-2180},
abstract = {BACKGROUND: Obesity is known to modulate human health in a number of ways including altering the microbiome of the gut. Very few studies have examined the how obesity may affect the microbiomes of sites distant to the gut. We hypothesized that vulva and abdominal skin may be especially susceptible to body mass index (BMI)-induced alterations in biophysical properties and the microbiome due increased maceration and skin folds at those sites. The aim of this study was to determine if high BMI (≥30) was associated with alterations in the biophysical properties and microbiomes of vulva and abdominal skin.

RESULTS: The vulvar microbial communities of healthy reproductive-aged females were examined using 16S rRNA sequencing techniques. Our results show that vulvar pH of women with high body mass index (BMI) was statistically higher than that of women with average BMI. Phylogenetic analysis of the vulvar microbiota indicated that women with average BMI have a predominately Lactobacillus-dominated flora, whereas women with high BMI and higher pH were predominately colonized by Finegoldia and Corynebacterium. This BMI-associated shift in microbiota was not observed in samples collected from the exposed skin around the belly, indicating the effect is not global.

CONCLUSION: These results indicate that physiological changes associated with changes in BMI may modulate the vulva microbiome.},
}

@article {pmid30654636,
year = {2019},
author = {Doulberis, M and Polyzos, SA and Papaefthymiou, A and Katsinelos, P and Kountouras, J},
title = {Comments to the Editor concerning the paper entitled "The microbiome and ophthalmic disease" by Baim et al.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {},
number = {},
pages = {1535370218824340},
doi = {10.1177/1535370218824340},
pmid = {30654636},
issn = {1535-3699},
}

@article {pmid30654634,
year = {2019},
author = {Casavant, SG and Cong, X and Fitch, RH and Moore, J and Rosenkrantz, T and Starkweather, A},
title = {Allostatic Load and Biomarkers of Stress in the Preterm Infant: An Integrative Review.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {1099800418824415},
doi = {10.1177/1099800418824415},
pmid = {30654634},
issn = {1552-4175},
abstract = {BACKGROUND:: Every year, an estimated 15 million babies are born preterm (<37 weeks' gestational age) globally. These preterm infants are exposed to repeated stressful and often painful procedures as part of routine life-saving care within the neonatal intensive care unit (NICU). Low thresholds for tactile and nociceptive input make it more difficult for neonates to discriminate between noxious and nonnoxious stimuli, which can result in continuous activation of stress responses in an attempt to achieve stability through adaptation, or allostasis. Rapidly reoccurring stressors can render stress-response systems over- or underactive, creating wear and tear, or allostatic load. A better understanding of biomarkers related to allostatic load might aid in early detection and prevention/alleviation of allostatic load in this population.

PURPOSE:: To identify stress biomarkers that have been studied in preterm infants at different time points in the NICU and as long-term outcome measures.

METHOD/SEARCH STRATEGY:: Systematic searches were conducted of PubMed, CINAHL, SCOPUS, and PsychInfo databases.

FINDINGS/RESULTS:: Twenty-one studies met inclusion criteria for this review. Several putative biomarkers were identified, including cortisol levels, epigenetic markers, brain microstructure, markers of oxidative stress, and the brain-gut-microbiome axis.

CONCLUSION:: The interaction of disease with therapeutic interventions may inadvertently increase infant allostatic load. In addition to human studies, future research should leverage newly available large data sets to conduct additional analyses.},
}

@article {pmid30654495,
year = {2019},
author = {Connelly, S and Parsley, T and Ge, H and Kaleko, M},
title = {Identification, Characterization, and Formulation of a Novel Carbapenemase Intended to Prevent Antibiotic-Mediated Gut Dysbiosis.},
journal = {Microorganisms},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/microorganisms7010022},
pmid = {30654495},
issn = {2076-2607},
abstract = {Antibiotics can damage the gut microbiome leading to opportunistic infections and the emergence of antibiotic resistance. Microbiome protection via antibiotic inactivation in the gastrointestinal (GI) tract represents a strategy to limit antibiotic exposure of the colonic microbiota. Proof of concept for this approach was achieved with an orally-administered beta-lactamase enzyme, SYN-004 (ribaxamase), that was demonstrated to degrade ceftriaxone excreted into the GI tract and protect the gut microbiome from antibiotic-mediated dysbiosis. Ribaxamase efficiently degrades penicillin and cephalosporin beta-lactam antibiotics, but is not active against carbapenems. To expand this microbiome protection strategy to include all classes of beta-lactams, three distinct carbapenemases were evaluated for manufacturability, antibiotic degradation spectrum, and stability in human intestinal fluid. E. coli production strains were generated for P2A, a novel metallo-enzyme isolated from B. cereus, New Delhi metallo-beta-lactamase (NDM), and Klebsiella pneumoniae carbapenemase (KPC). While all three enzymes effectively inactivated a broad range of antibiotics, including penicillins, most cephalosporins, and carbapenems in vitro, only P2A retained biological activity when incubated with human chyme. As functional stability in the intestinal tract is a key requirement for an orally-delivered enzyme, P2A was chosen as a potential clinical candidate. An enteric formulation of P2A was developed, called SYN-006, that was inert under high acid conditions, with enzyme dissolution occurring at pH > 5.5. SYN-006 has the potential to expand microbiome protection via antibiotic inactivation to include all classes of beta-lactam antibiotics.},
}

@article {pmid30654045,
year = {2019},
author = {Toivonen, L and Camargo, CA and Gern, JE and Bochkov, YA and Mansbach, JM and Piedra, PA and Hasegawa, K},
title = {Association between rhinovirus species and nasopharyngeal microbiota in infants with severe bronchiolitis.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.12.1004},
pmid = {30654045},
issn = {1097-6825},
abstract = {Among 774 infants with severe bronchiolitis, rhinovirus species related to distinct nasopharyngeal microbiota. Infants with rhinovirus-A were more likely to have Haemophilus-dominant microbiota profile, while those with rhinovirus-C were more likely to have Moraxella-dominant profile.},
}

@article {pmid30653931,
year = {2019},
author = {Vuong, HE and Hsiao, EY},
title = {Gut Microbes Join the Social Network.},
journal = {Neuron},
volume = {101},
number = {2},
pages = {196-198},
doi = {10.1016/j.neuron.2018.12.035},
pmid = {30653931},
issn = {1097-4199},
abstract = {The gut microbiome is increasingly implicated in the regulation of social behavior across model organisms. In this issue of Neuron, Sgritta et al. (2018) examine the role of the gut microbiome in social reward circuits and sociability in three mouse models of autism spectrum disorder.},
}

@article {pmid30653021,
year = {2019},
author = {Niederberger, C},
title = {Re: Testicular Microbiome in Azoospermic Men-First Evidence of the Impact of an Altered Microenvironment.},
journal = {The Journal of urology},
volume = {},
number = {},
pages = {},
doi = {10.1097/01.JU.0000553265.88701.d4},
pmid = {30653021},
issn = {1527-3792},
}

@article {pmid30652494,
year = {2019},
author = {Kalantar, KL and Moazed, F and Christenson, SC and Wilson, J and Deiss, T and Belzer, A and Vessel, K and Caldera, S and Jauregui, A and Bolourchi, S and DeRisi, JL and Calfee, CS and Langelier, C},
title = {A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota.},
journal = {American journal of physiology. Lung cellular and molecular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajplung.00476.2018},
pmid = {30652494},
issn = {1522-1504},
abstract = {Accurate and informative microbiologic testing is essential for guiding diagnosis and management of pneumonia in critically ill patients. Sampling of tracheal aspirate (TA) is less invasive compared to mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in mechanically ventilated patients, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture, and as such provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to quantitatively assess the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences betweensampletypes across all subjects, however we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by a dominant pathogen. In addition, we found that both mBAL and TA were similar in terms of microbialrelative abundance, abundance of oropharyngeal taxa, and microbial diversity. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL, and that this similarity is most significant in the setting of bacterial pneumonia.},
}

@article {pmid30652422,
year = {2019},
author = {Pearson, T and Caporaso, JG and Yellowhair, M and Bokulich, NA and Padi, M and Roe, DJ and Wertheim, BC and Linhart, M and Martinez, JA and Bilagody, C and Hornstra, H and Alberts, DS and Lance, P and Thompson, PA},
title = {Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development.},
journal = {Cancer medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/cam4.1965},
pmid = {30652422},
issn = {2045-7634},
support = {NIH/NCI U54CA143924//Native American Cancer Prevention/ ; U54CA143925//Native American Cancer Prevention/ ; 1565100//NSF/ ; R01 CA151708//NSF/ ; P30 CA023074/BC/NCI NIH HHS/United States ; },
abstract = {It has been previously reported that ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduced risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colorectal cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Using banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal adenomatous polyps, we compared change in the microbiome composition after a 3-year intervention in a subset of participants randomized to oral UDCA at 8-10 mg/kg of body weight per day (n = 198) or placebo (n = 203). Study participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This reflected a UDCA-associated shift in microbial community composition (P < 0.001), independent of sex, with no evidence of a UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P > 0.05) in men or women. Separate analyses of microbial networks revealed an overrepresentation of Faecalibacterium prausnitzii in the post-UDCA arm and an inverse relationship between F prausnitzii and Ruminococcus gnavus. In men who received UDCA, the overrepresentation of F prausnitzii and underrepresentation of R gnavus were more prominent in those with no adenoma recurrence at follow-up compared to men with recurrence. This relationship was not observed in women. Daily UDCA use modestly influences the relative abundance of microbial species in stool and affects the microbial network composition with suggestive evidence for sex-specific effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.},
}

@article {pmid30652367,
year = {2019},
author = {Romero, S and Nastasa, A and Chapman, A and Kwong, WK and Foster, LJ},
title = {The Honey Bee Gut Microbiota: Strategies for Study and Characterization.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12567},
pmid = {30652367},
issn = {1365-2583},
abstract = {Gut microbiota research is an emerging field that improves our understanding of the ecological and functional dynamics of gut environments. The honey bee gut microbiota is a highly rewarding community to study, as honey bees are critical pollinators of many crops for human consumption and produce valuable commodities such as honey and wax. Most significantly, unique characteristics of the Apis mellifera gut habitat make it a valuable model system. This review discusses methods and pipelines used in the study of the gut microbiota of A. mellifera and closely related species for four main purposes: identifying microbiota taxonomy, characterizing microbiota genomes (microbiome), characterizing microbiota-microbiota interactions, and identifying functions of the microbial community in the gut. The purpose of this contribution is to increase understanding of honey bee gut microbiota, to facilitate bee microbiota and microbiome research in general, and to aid design of future experiments in this growing field. This article is protected by copyright. All rights reserved.},
}

@article {pmid30652107,
year = {2018},
author = {Soderborg, TK and Friedman, JE},
title = {Imbalance in gut microbes from babies born to obese mothers increases gut permeability and myeloid cell adaptations that provoke obesity and NAFLD.},
journal = {Microbial cell (Graz, Austria)},
volume = {6},
number = {1},
pages = {102-104},
doi = {10.15698/mic2019.01.666},
pmid = {30652107},
issn = {2311-2638},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease affecting nearly 40% of obese youth and up to 10% of the general pediatric population. A key aspect of NAFLD pathogenesis is proinflammatory hepatic macrophage activation and hepatic recruitment of circulating monocytes, which originate from the bone marrow. In neonates, the activation and polarization of myeloid immune cells are normally shaped in part by systemic factors derived from intestinal microbiota during the first 1000 days of life. Perturbations of the gut microbiome, and in turn the metabolites and bacterial products released systemically, can affect the functional phenotype of these immune cells. Evidence in germ-free mice has shown that fecal microbial transfer from obese mice or obese human donors promotes obesity and inflammation in the recipients, suggesting a direct role for the gut microbiome in promoting obesity and possibly NAFLD. Indeed, patients suffering from NAFLD show evidence for dysbiosis, increased gut permeability, and changes in bile acids that drive the progression of hepatic inflammation toward non-alcoholic steatohepatitis (NASH), the more severe form of the disease. Compared with infants born to normal-weight mothers, we previously showed that the gut microbiome from neonates born to obese mothers is compositionally distinct. However, whether this alteration in early gut microbiota in infants born to obese mothers can cause inflammatory processes that initiate development of NAFLD or obesity is unknown. How these alterations contribute to long-term immune cell mediated liver inflammation and progression of NAFLD needs to be determined. Our recently published work (Soderborg et al., Nat Commun 9:4462) demonstrates a causative role of early life microbiome dysbiosis in infants born to mothers with obesity in novel pathways that promote developmental programming of NAFLD.},
}

@article {pmid30652093,
year = {2018},
author = {Shigematsu, Y and Inamura, K},
title = {Gut microbiome: a key player in cancer immunotherapy.},
journal = {Hepatobiliary surgery and nutrition},
volume = {7},
number = {6},
pages = {479-480},
doi = {10.21037/hbsn.2018.10.02},
pmid = {30652093},
issn = {2304-3881},
}

@article {pmid30651985,
year = {2019},
author = {Guevarra, RB and Lee, JH and Lee, SH and Seok, MJ and Kim, DW and Kang, BN and Johnson, TJ and Isaacson, RE and Kim, HB},
title = {Piglet gut microbial shifts early in life: causes and effects.},
journal = {Journal of animal science and biotechnology},
volume = {10},
number = {},
pages = {1},
doi = {10.1186/s40104-018-0308-3},
pmid = {30651985},
issn = {1674-9782},
abstract = {The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets.},
}

@article {pmid30651726,
year = {2018},
author = {Bencard, A and Whiteley, LE},
title = {Mind the Gut-displaying microbiome research through artistic collaboration.},
journal = {Microbial ecology in health and disease},
volume = {29},
number = {2},
pages = {1555433},
doi = {10.1080/16512235.2018.1555433},
pmid = {30651726},
issn = {0891-060X},
abstract = {This paper presents the Mind the Gut exhibition, opened in 2017 at the Medical Museion, the University of Copenhagen's museum for the culture and history of medicine. It is an experimental exhibition combining science, art, and history in an examination of the relationship between mind and gut, including the trillions of microbes that inhabits them. Mind the Gut was the result of a 2-year-long research and curatorial process, which began in 2015 when Museion was awarded the Bikuben Foundation Vision Award. The exhibition brings together the long history of attempts to understand and intervene in the relationship between mind and gut, between emotions and digestion with cutting-edge biomedical research, and includes the perspectives of science, medicine, and personal experience, via a combination of artworks, historical objects from the Medical Museion collections, items from laboratories, and individual stories. The exhibition is organized around different ways the body has been handled in order to intervene in interactions between mind, gut, and bacteria, including imaging, electrifying, feeding, drugging, and opening surgically. This paper outlines some of the thoughts on science communication that motivated the exhibition, discussing why the displays emphasize the exploratory over the explanatory. Also discussed are several artistic collaborations that formed part of the displays. Ultimately, Mind the Gut is created to be a public space that encourages reflection and curiosity, by showing how biomedicine fits into social, cultural, historical, and directly personal contexts. The exhibition does not aim to provide answers about what food the visitors should eat or what the truth of how gut and brain interactions might be. Rather, it emphasizes process over result, hopefully encouraging the visitors to ask their own questions of the relationship between mind and gut, between body and microbes.},
}

@article {pmid30651683,
year = {2018},
author = {Shah, S},
title = {Salivaomics: The current scenario.},
journal = {Journal of oral and maxillofacial pathology : JOMFP},
volume = {22},
number = {3},
pages = {375-381},
doi = {10.4103/jomfp.JOMFP_171_18},
pmid = {30651683},
issn = {0973-029X},
abstract = {For generations, blood has been the medium of choice for diagnosing most diseases and conditions. The reason for this is mainly the limitations of technology. The concept of oral diagnostics is preferred to more invasive methods. In recent years, it has become evident that the salivary constituents become detectably altered in response to certain disease states. Even so, what is most impressive is that salivary biomarkers not only arise in correlation with oral disorders but also those of distal tissues and organs. This suggests that oral fluids may represent a substantial reservoir of molecular and microbial information capable of communicating the onset or presence of disease throughout the body. An initiative of the National Institute of Dental and Craniofacial Research created a roadmap to achieve these goals whereby, with the use of oral fluids as the diagnostic medium, it would become possible to scrutinize the health and/or disease status of patients. The real promise of salivary analysis use is the ability of the patient or clinician to directly and continuously assess disease status, progression and therapeutic efficacy. The sensitive analysis may even allow presymptomatic diagnosis. There are five major diagnostic alphabets available in saliva namely, proteins, messenger RNAs, micro-RNAs (mi-RNAs), metabolic compounds and microbes which offer substantial advantages for salivary diagnostics because, the state of the disease may be associated with detectable changes in one, but not all, dimensions. Recently, the Salivaomics Knowledge Base (SKB) has been established by aligning the salivary biomarker discovery. The SKB constitutes data repository, management system and web resource fabricated to support human salivary proteomics, transcriptomics, miRNA, metabolomics and microbiome research.},
}

@article {pmid30651577,
year = {2019},
author = {Goethel, A and Turpin, W and Rouquier, S and Zanello, G and Robertson, SJ and Streutker, CJ and Philpott, DJ and Croitoru, K},
title = {Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41385-018-0128-y},
pmid = {30651577},
issn = {1935-3456},
abstract = {Inflammatory bowel disease (IBD) etiology involves genetic susceptibility, environmental triggers, and the gut microbiome. Antibiotic exposure is associated with IBD, both in early life and adulthood. Here, we investigated whether Nod2-deficiency influenced response of the gut microbiota to antibiotics and subsequent colitis susceptibility. Wild-type and Nod2-/- littermate mice were treated with amoxicillin as adults or neonates, and fecal samples were collected for 16S rRNA sequencing. Five weeks after antibiotic exposure, dextran sulfate sodium (DSS) colitis was induced. Antibiotic treatment altered the microbiota of adult WT and Nod2-/- mice, but recovery was delayed in Nod2-/- mice. Neonatal antibiotic treatment significantly changed the microbiota at weaning in WT and Nod2-/- littermates; however, Nod2-/- mice maintained reduced microbial diversity 14 days after cessation of antibiotics. Although treatment of adult mice did not influence susceptibility to colitis, neonatally treated Nod2-/- mice developed a more severe colitis. Moreover, the colitis phenotype was transferable through fecal transplantation into germ-free Nod2-/- recipients, and was associated with changes in intestinal T cells and the cytokine milieu following inflammation. These data demonstrate that neonatal antibiotic exposure has long-lasting influence on the microbiota and mucosal immunity, and may explain how NOD2 contributes to the risk of intestinal inflammation.},
}

@article {pmid30651402,
year = {2019},
author = {Mu, A and Kwong, JC and Isles, NS and Gonçalves da Silva, A and Schultz, MB and Ballard, SA and Lane, CR and Carter, GP and Williamson, DA and Seemann, T and Stinear, TP and Howden, BP},
title = {Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.},
journal = {mSphere},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/mSphere.00529-18},
pmid = {30651402},
issn = {2379-5042},
abstract = {Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium.IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.},
}

@article {pmid30651010,
year = {2019},
author = {Metz, TD and McKinney, J and Allshouse, AA and Doucette Knierim, S and Carey, JC and Heyborne, KD},
title = {Exposure to group B streptococcal antibiotic prophylaxis and early childhood body mass index in a vaginal birth cohort.},
journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {},
number = {},
pages = {1-171},
doi = {10.1080/14767058.2019.1571575},
pmid = {30651010},
issn = {1476-4954},
abstract = {OBJECTIVE: Perinatal antibiotic exposure may be associated with changes in both early infancy gut microbiota and later childhood obesity. Our objective was to evaluate if group B Streptococcus (GBS) antibiotic prophylaxis is associated with higher body mass index (BMI) in early childhood.

METHODS: Retrospective cohort study of mother/child dyads in a single hospital system over a 6-year period. All women with term, singleton, vertex, vaginal deliveries who received no antibiotics or received antibiotics only for GBS prophylaxis and whose children had BMIs available at 2-5 years of age were included. Children were divided into three groups for comparison: children born to GBS positive mothers that received antibiotics solely for GBS prophylaxis, children born to GBS negative women that received no antibiotics (healthy controls), and children born to GBS positive mothers who received no antibiotics. The primary outcome was the earliest available child BMI Z-score at 2-5 years of age. Multivariable linear regression was used to estimate differences in child BMI Z-scores between groups, adjusted for maternal BMI, age, race, parity, tobacco use, and child birthweight.

RESULTS: Of 4825 women, 786 (16.3%) were GBS positive and received prophylactic antibiotics, 3916 (81.2%) were GBS negative and received no antibiotics, and 123 (2.5%) were GBS positive but received no antibiotics. Childhood BMI Z-scores were similar between children exposed to intrapartum GBS prophylaxis and healthy controls who were unexposed in both unadjusted (mean (SE), 0.04 (0.04) versus -0.3 (0.02), p = 0.11) and adjusted (0.01 (0.05) versus -0.04 (0.03), p = 0.3) models.

CONCLUSIONS: Exposure to intrapartum antibiotic prophylaxis for GBS was not associated with higher early childhood BMI Z-scores compared to healthy controls.},
}

@article {pmid30650376,
year = {2019},
author = {Pronovost, GN and Hsiao, EY},
title = {Perinatal Interactions between the Microbiome, Immunity, and Neurodevelopment.},
journal = {Immunity},
volume = {50},
number = {1},
pages = {18-36},
doi = {10.1016/j.immuni.2018.11.016},
pmid = {30650376},
issn = {1097-4180},
abstract = {The microbiome modulates host immune function across the gastrointestinal tract, peripheral lymphoid organs, and central nervous system. In this review, we highlight emerging evidence that microbial effects on select immune phenotypes arise developmentally, where the maternal and neonatal microbiome influence immune cell ontogeny in the offspring during gestation and early postnatal life. We further discuss roles for the perinatal microbiome and early-life immunity in regulating normal neurodevelopmental processes. In addition, we examine evidence that abnormalities in microbiota-neuroimmune interactions during early life are associated with altered risk of neurological disorders in humans. Finally, we conclude by evaluating the potential implications of microbiota-immune interventions for neurological conditions. Continued progress toward dissecting mechanistic interactions between the perinatal microbiota, immune system, and nervous system might uncover fundamental insights into how developmental interactions across physiological systems inform later-life health and disease.},
}

@article {pmid30650116,
year = {2019},
author = {Akami, M and Andongma, AA and Zhengzhong, C and Nan, J and Khaeso, K and Jurkevitch, E and Niu, CY and Yuval, B},
title = {Intestinal bacteria modulate the foraging behavior of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae).},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210109},
doi = {10.1371/journal.pone.0210109},
pmid = {30650116},
issn = {1932-6203},
abstract = {The gut microbiome of insects directly or indirectly affects the metabolism, immune status, sensory perception and feeding behavior of its host. Here, we examine the hypothesis that in the oriental fruit fly (Bactrocera dorsalis, Diptera: Tephritidae), the presence or absence of gut symbionts affects foraging behavior and nutrient ingestion. We offered protein-starved flies, symbiotic or aposymbiotic, a choice between diets containing all amino acids or only the non-essential ones. The different diets were presented in a foraging arena as drops that varied in their size and density, creating an imbalanced foraging environment. Suppressing the microbiome resulted in significant changes of the foraging behavior of both male and female flies. Aposymbiotic flies responded faster to the diets offered in experimental arenas, spent more time feeding, ingested more drops of food, and were constrained to feed on time-consuming patches (containing small drops of food), when these offered the full complement of amino acids. We discuss these results in the context of previous studies on the effect of the gut microbiome on host behavior, and suggest that these be extended to the life history dimension.},
}

@article {pmid30649912,
year = {2019},
author = {Liu, H and Wang, Y and Sun, D and Jiang, H and Yang, F},
title = {Insight into the correlation between biochar amendment and shift in bacterial community four years after a single incorporation in soybean/maize-planted soils in north-eastern China.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2018-0366},
pmid = {30649912},
issn = {1480-3275},
abstract = {To date, there have been comparatively few reports addressing the correlation between biochar treatments, crop species and microbiome shifts. In this study, the shifts in soil bacterial community were investigated four years after a single incorporation of biochar in soybean- and maize-planted soils. Clear changes in bacterial community composition and structure were detected in the soybean-planted soil amended with low-titer biochar (7.89 t/ha), whereas such changes in the maize-planted soil were not observed at the same biochar amendment rate, suggesting a more sensitive influence on bacterial community in the soybean-planted soil than that in the maize-planted soil. The bacterial abundance in the maize-planted soil was reduced significantly with the increasing biochar addition (15.78 t/ha and 47.34 t/ha), which was probably due to the substances inhibition originated from biochar. Both the bacterial community and biomarkers in soil under biochar amendment varied with planted crops, which mean different responses of bacterial community to biochar amendment. All these results suggested that biochar might influence bacterial community in maize- and soybean-growing soils under different mechanisms. Our findings should be valuable for in-depth understanding the potential mechanism of soil microbiome changes following biochar incorporation and for biochar application in agriculture.},
}

@article {pmid30649714,
year = {2019},
author = {Baranowski, T and Motil, KJ and Moreno, JP},
title = {Multi-etiological Perspective on Child Obesity Prevention.},
journal = {Current nutrition reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13668-019-0256-3},
pmid = {30649714},
issn = {2161-3311},
support = {58-3092-5-001//Agricultural Research Service/ ; },
abstract = {PURPOSE OF REVIEW: The simple energy balance model of obesity is inconsistent with the available findings on obesity etiology, prevention, and treatment. Yet, the most commonly stated causes of pediatric obesity are predicated on this model. A more comprehensive biological model is needed upon which to base behavioral interventions aimed at obesity prevention. In this light, alternative etiologies are little investigated and thereby poorly understood.

RECENT FINDINGS: Three candidate alternate etiologies are briefly presented: infectobesity, the gut microbiome, and circadian rhythms. Behavioral child obesity preventive investigators need to collaborate with biological colleagues to more intensively analyze the behavioral aspects of these etiologies and to generate innovative procedures for preventing a multi-etiological problem, e.g., group risk analysis, triaging for likely causes of obesity.},
}

@article {pmid30649314,
year = {2019},
author = {Kostanjšek, R and Prodan, Y and Stres, B and Trontelj, P},
title = {Composition of the cutaneous bacterial community of a cave amphibian, Proteus anguinus.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz007},
pmid = {30649314},
issn = {1574-6941},
abstract = {The European cave salamander Proteus anguinus is a charismatic amphibian endemic to the concealed and inaccessible subterranean waters of the Dinaric Karst. Despite its exceptional conservation importance not much is known about its ecology and interactions with the groundwater microbiome. The cutaneous microbiota of amphibians is an important driver of metabolic capabilities and immunity, and thus a key factor of their wellbeing and survival. We used high-throughput 16S rRNA gene sequencing based on seven variable regions to examine the bacteriome of the skin of five distinct evolutionary lineages of P. anguinus and in their groundwater environment. The skin bacteriomes turned out to be strongly filtered subsamples of the environmental microbial community. The resident microbiota of the analyzed individuals was dominated by five bacterial taxa. Despite an indicated functional redundancy, the cutaneous bacteriome of P. anguinus presumably provides protection against invading microbes by occupying the niche, and thus could serve as indicator of health status. Besides conservation implications for P. anguinus, our results provide a baseline for future studies on other endangered neotenic salamanders.},
}

@article {pmid30649204,
year = {2019},
author = {Saha, S and Johnson, J and Pal, S and Weinstock, G and Rajasekaran, S},
title = {MSC: a metagenomic sequence classification algorithm.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/bty1071},
pmid = {30649204},
issn = {1367-4811},
abstract = {Motivation: Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing (NGS) technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbe genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article we propose a highly efficient metagenomic sequence classification algorithm (MSC) that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the target sequences.

Results: Microbiome researchers are generally interested in two objectives of a taxonomic classifier: 1) to detect prevalence, i.e., the taxa present in a sample, and 2) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory, and runtime. Moreover, MSC outputs an approximate estimate of the abundances.

Availability: The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.},
}

@article {pmid30649168,
year = {2019},
author = {Griffith, JC and Morgan, XC},
title = {Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwz007},
pmid = {30649168},
issn = {1476-6256},
abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference dataset of the "normal" human microbiome of 242 healthy adults at five major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP dataset still presents technical and bioinformatic challenges, as researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. In this issue, the HMP16SData R/Bioconductor package developed by Schiffer and colleagues (Am J Epidemiol. XXX; XX (XX): XX-XXX) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved dbGaP projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools. This will translate to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.},
}

@article {pmid30649166,
year = {2019},
author = {Schiffer, L and Azhar, R and Shepherd, L and Ramos, M and Geistlinger, L and Huttenhower, C and Dowd, JB and Segata, N and Waldron, L},
title = {HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwz006},
pmid = {30649166},
issn = {1476-6256},
abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 239 healthy American adults, to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly-available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.},
}

@article {pmid30649054,
year = {2019},
author = {Maurice, JB and Garvey, L and Tsochatzis, EA and Wiltshire, M and Cooke, G and Guppy, N and McDonald, J and Marchesi, J and Nelson, M and Kelleher, P and Goldin, R and Thursz, M and Lemoine, M},
title = {Monocyte-Macrophage activation is associated with NAFLD and liver fibrosis in HIV mono-infection independently of the gut microbiome and bacterial translocation.},
journal = {AIDS (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAD.0000000000002133},
pmid = {30649054},
issn = {1473-5571},
abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is common among people living with HIV. There is limited data available on the pathophysiology of NAFLD and the development of fibrosis in this population.

OBJECTIVES: to investigate the association of bacterial translocation, adipose tissue dysfunction, monocyte activation and gut dysbiosis in patients with HIV mono-infection and NAFLD.

METHODS: Cases with biopsy-proven NAFLD and HIV mono-infection were age and sex-matched to HIV+ and HIV- controls. Markers of bacterial translocation (lipopolysaccharide-binding protein (LBP), bacterial DNA and lipopolysaccharide (LPS)), adipose tissue dysfunction (leptin, adiponectin) and monocyte activation (sCD14 and sCD163) were measured by ELISA. Hepatic patterns of macrophage activation were explored with immunohistochemistry. 16 s rRNA sequencing was performed with stool.

RESULTS: Thirty-three cases were included (≥F2 fibrosis n = 16), matched to HIV+ (n = 29) and HIV- (n = 17) controls. Cases with NAFLD were more obese (BMI 31.0 ± 4.4 kg/m vs 24.1 ± 2.8 kg/m p < 0.001) and had significantly increased levels of sCD14, sCD163 and higher leptin to adiponectin ratio versus HIV+ controls. Cases with ≥F2 verses < F2 fibrosis had increased sCD14 (1.4 ± 0.4 vs 1.1 ± 0.3 μg/ml, p = 0.023) and sCD163 (1.0 ± 0.3 vs 0.8 ± 0.3 μg/ml, p = 0.060) which correlated with waist circumference (sCD14 p = 0.022, sCD163 p = 0.011). Immunohistochemistry showed increased hepatic portal macrophage clusters in patients with fibrosis. No markers of bacterial translocation or changes to the microbiome were associated with NAFLD or fibrosis.

CONCLUSION: NAFLD fibrosis stage in HIV mono-infected patients is associated with monocyte activation in the context of obesity, which may be independent of bacterial translocation and gut microbiome.},
}

@article {pmid30649052,
year = {2019},
author = {Cook, RR and Fulcher, JA and Tobin, NH and Li, F and Lee, D and Javanbakht, M and Brookmeyer, R and Shoptaw, S and Bolan, R and Aldrovandi, GM and Gorbach, PM},
title = {Effects of HIV viremia on the gastrointestinal microbiome of young men who have sex with men.},
journal = {AIDS (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAD.0000000000002132},
pmid = {30649052},
issn = {1473-5571},
abstract = {OBJECTIVE: We employed a high-dimensional covariate adjustment method in microbiome analysis to better control for behavioral and clinical confounders, and in doing so examine the effects of HIV on the rectal microbiome.

DESIGN: Three hundred eighty-three men who have sex with men were grouped into four HIV viremia categories: HIV negative (n = 200), HIV+ undetectable (HIV RNA < 20 copies/mL; n = 66), HIV+ suppressed (RNA 20-200 copies/mL; n = 72) and HIV+ viremic (RNA > 200 copies/mL; n = 45).

METHODS: We performed 16S rRNA gene sequencing on rectal swab samples and used inverse probability of treatment-weighted marginal structural models to examine differences in microbial composition by HIV viremia category.

RESULTS: HIV viremia explained a significant amount of variability in microbial composition in both unadjusted and covariate-adjusted analyses (R = .011, p = .02). Alterations in bacterial taxa were more apparent with increasing viremia. Relative to the HIV negative group, HIV+ undetectable participants showed depletions in Brachyspira, Campylobacter, and Parasutterella while suppressed participants demonstrated depletions in Barnesiella, Brachyspira and Helicobacter. The microbial signature of viremic men was most distinct, showing enrichment in inflammatory genera Peptoniphilus, Porphyromonas, and Prevotella and depletion of Bacteroides, Brachyspira, and Faecalibacterium, among others.

CONCLUSIONS: Our study shows that, after accounting for the influence of multiple confounding factors, HIV is associated with dysbiosis in the gastrointestinal microbiome in a dose-dependent manner. This analytic approach may allow for better identification of true microbial associations by limiting the effects of confounding, and thus improve comparability across future studies.},
}

@article {pmid30648974,
year = {2019},
author = {Deng, F and Li, Y and Zhao, J},
title = {The gut microbiome of healthy long-living people.},
journal = {Aging},
volume = {},
number = {},
pages = {},
doi = {10.18632/aging.101771},
pmid = {30648974},
issn = {1945-4589},
}

@article {pmid30648419,
year = {2019},
author = {BenIsrael, M and Wanner, P and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE},
title = {Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/15226514.2018.1523873},
pmid = {30648419},
issn = {1549-7879},
abstract = {Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase. Enrichment of 13C from toluene in the vapor phase compared to groundwater provided evidence for biodegradation in the vadose zone. Total bacterial abundance (16S rRNA) and abundance and expression of degradation genes were determined in rhizosphere soil (DNA and RNA) and roots (DNA) using quantitative PCR. Relative abundances of degraders in the rhizosphere were on average higher at greater depths, except for enrichment of PHE-encoding communities that more strongly followed patterns of toluene concentrations detected. Quantification of RMO and PHE gene transcripts supported observations of active aerobic toluene degradation. Finally, spatially-variable numbers of toluene degraders were detected in poplar roots. We present multiple lines of evidence for biodegradation in the vadose zone at this site, contributing to our understanding of mechanisms of action of the phytoremediation system.},
}

@article {pmid30648012,
year = {2019},
author = {Wu, SH and Huang, BH and Gao, J and Wang, S and Liao, PC},
title = {The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6147},
doi = {10.7717/peerj.6147},
pmid = {30648012},
issn = {2167-8359},
abstract = {Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.},
}

@article {pmid30647970,
year = {2018},
author = {Zam, W},
title = {Gut Microbiota as a Prospective Therapeutic Target for Curcumin: A Review of Mutual Influence.},
journal = {Journal of nutrition and metabolism},
volume = {2018},
number = {},
pages = {1367984},
doi = {10.1155/2018/1367984},
pmid = {30647970},
issn = {2090-0724},
abstract = {Background: Turmeric is a spice that has recently received much interest and has been widely used in Ayurvedic medicine. Turmeric products are diarylheptanoids and have been characterized as safe. They are termed as curcuminoids that consists essentially of three major compounds: curcumin, demethoxycurcumin, and bisdemethoxycurcumin. Curcumin is a lipophilic polyphenol that has poor systemic bioavailability and suffers from biotransformation by human intestinal microflora to yield different metabolites that are easily conjugated to glucuronides and sulfate O-conjugated derivatives. Recently, an increasing number of studies have indicated that dysbiosis is linked with many metabolic diseases, though gut microbiota could be a novel potential therapeutic target.

Scope and Approach: Thus, it is suspected that curcumin and its derivatives exert direct regulative effects on the gut microbiota which could explain the paradox between curcumin's poor systemic bioavailability and its widely reported pharmacological activities.

Key Findings and Conclusions: This article summarizes a range of studies that highlight the interaction between curcumin and gut microbiota and considers opportunities for microbiome-targeting therapies using turmeric extract.},
}

@article {pmid30647905,
year = {2018},
author = {Bullerdiek, J and Rommel, B},
title = {Factors targeting MED12 to drive tumorigenesis?.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {359},
doi = {10.12688/f1000research.14227.1},
pmid = {30647905},
issn = {2046-1402},
abstract = {Mediator Subcomplex 12 (MED12) is part of the transcriptional preinitiation machinery. Mutations of its gene predominantly occur in two types of highly frequent benign tumors, uterine leiomyomas and fibroadenomas of the breast, where they apparently act as driver mutations. Nevertheless, their presence is not restricted to benign tumors having been found at considerable frequencies in uterine leiomyosarcomas, malignant phyllodes tumors, and chronic lymphocytic leukemia also. Most of the mutations are located within exon 2 of the gene but in rare cases the intron 1/exon 2 boundary or exon 1 are affected. As to their type, predominantly single nucleotide exchanges with a hotspot in one codon are found, but small deletions clustering around that hotspot also are not uncommon. According to their presumed classification as gain-of-function mutations, these latter deletions are leaving the open reading frame intact. As to the types of mutations, so far no apparent differences between the tumor entities affected have emerged. Interestingly, this pattern with small deletions clustered around the hotspot of single nucleotide exchanges resembles that seen as a result of targeted gene editing. In contrast to other driver mutations the percentage of MED12-mutation positive tumors of independent clonal origin increases with the number of tumors per patient suggesting unknown etiological factors supporting site specific mutagenesis. These factors may act by inducing simultaneous site-specific double strand breaks the erroneous repair of which may lead to corresponding mutations. As inducers of DNA damage and its repair such as foreign nucleic acids of the microbiome displaying sequence homology to the putative target site might play a role. Interestingly, a 16 base pair homology of the hotspot to a putative terminator base-paired hairpin sequence of a Staphylococcus aureus tRNA gene cluster has been noted which might form R-loop like structures with its target sequence thus inducing said changes.},
}

@article {pmid30647128,
year = {2019},
author = {Alimov, I and Menon, S and Cochran, N and Maher, R and Wang, Q and Alford, J and Concannon, JB and Yang, Z and Harrington, E and Llamas, L and Lindeman, A and Hoffman, G and Schuhmann, T and Russ, C and Reece-Hoyes, J and Canham, SM and Cai, X},
title = {Bile acid analogues are activators of Pyrin inflammasome.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA118.005103},
pmid = {30647128},
issn = {1083-351X},
abstract = {Bile acids are critical metabolites in the gastrointestinal tract which contribute to maintaining intestinal immune homeostasis through crosstalk with the gut microbiota. The conversion of bile acids by the gut microbiome is now recognized as a factor affecting both host metabolism and immune responses, but its physiological roles remain unclear. We conducted a screen for microbiome metabolites that would function as inflammasome activators and herein report the identification of 12-oxo-lithocholic acid, (BAA485), a potential microbiome-derived bile acid metabolite. We demonstrate the more potent analog 11-oxo-12S-hydroxy lithocholic acid methyl ester (BAA473) can induce secretion of interleukin-18 (IL18) through activation of the inflammasome in both myeloid and intestinal epithelial cells. Using a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen with compound induced pyroptosis in THP-1 cells, we identified inflammasome activation by BAA473 is Pyrin-dependent (MEFV). To our knowledge, the bile acid analogues BAA485 and BAA473 are the first small molecule activators of the Pyrin inflammasome. We surmise that Pyrin inflammasome activation through microbiota-modified bile acid metabolites such as BAA473 and BAA485 plays a role in gut microbiota regulated intestinal immune response. The discovery of these two bioactive compounds may help further unveil the importance of Pyrin in gut homeostasis and autoimmune diseases.},
}

@article {pmid30646834,
year = {2019},
author = {Vallianou, NG and Tzortzatou-Stathopoulou, F},
title = {Microbiota and cancer: an update.},
journal = {Journal of chemotherapy (Florence, Italy)},
volume = {},
number = {},
pages = {1-5},
doi = {10.1080/1120009X.2018.1541046},
pmid = {30646834},
issn = {1973-9478},
abstract = {The number of microbes in the human intestine is approximately 1 × 1014, while the number of eukaryotic cells in the human body is around 1 × 1013. As a result of co-evolution of the host mucosal immune system and the microbiota, both have developed multiple mechanisms to maintain homeostasis. Nevertheless, when these mechanisms are disturbed by pathogenic bacteria, which invade this fragile environment, the immune system responds to the microbiota and may support tumour growth in the intestine. Data advocate that the microbiota and its interactions with the host could also be implicated in carcinogenesis in other organs. It is nowadays suggested that developing methods to selectively manipulate components of the microbiota and ultimately target tumorigenesis represents a complex but exciting challenge. In this review, the main pathogenetic mechanisms of the interplay between the microbiome and the innate system, which may be implicated in tumorigenesis are discussed. Also, the importance of the gut microbiota regarding efficacy and toxicity of current chemotherapeutic agents, as well as the direct antitumor properties of the microbiota, will be reviewed.},
}

@article {pmid30646486,
year = {2019},
author = {Chen, S and Ou, Y and Zhao, L and Li, Y and Qiao, Z and Hao, Y and Ren, F},
title = {Differential Effects of Lactobacillus casei Strain Shirota on Patients With Constipation Regarding Stool Consistency in China.},
journal = {Journal of neurogastroenterology and motility},
volume = {25},
number = {1},
pages = {148-158},
doi = {10.5056/jnm17085},
pmid = {30646486},
issn = {2093-0879},
abstract = {Background/Aims: Probiotics are expected to confer benefits on patients with constipation, but how probiotics act on constipated patients with variable stool consistencies remains unclear. We investigated the effect of Lactobacillus casei strain Shirota (LcS) on constipation-related symptoms, especially stool consistency, of constipated patients.

Methods: Constipated patients meeting the Rome III criteria were divided into 3 groups according to the Bristol Stool Form Scale (BSFS): hard (hard stool [HS], BSFS ＜ 3), normal (normal stool [NS], ≤ 3 BSFS ≤ 4), and soft (soft stool [SS], 4 ＜ BSFS ≤ 5) stools. Subjects in each group consumed a probiotic beverage containing 10¹⁰ colony-forming units of LcS daily for 28 days.

Results: LcS intervention significantly alleviated constipation-related symptoms and increased defecation frequency in all subjects. Four weeks of LcS supplementation softened the hard stools in HS, hardened the soft stools in SS, and did not alter the ideal stool consistency in NS. The short-chain fatty acid (SCFA) concentrations were highest in SS, followed by NS and HS. LcS intervention increased the stool SCFA levels in HS but reduced or did not alter the levels in NS and SS. LcS intervention increased the Pseudobutyrivibrio and Roseburia abundances in HS and decreased the Pseudobutyrivibrio abundance in SS.

Conclusions: LcS supplementation improved the constipation-related symptoms in constipated subjects. Differences in baseline stool consistency could result in different anti-constipation effects of LcS intervention. LcS balanced the stool consistency-softened the HS and hardened the SS. These effects could be associated with modulation of the gut microbiota and SCFA production.},
}

@article {pmid30646475,
year = {2019},
author = {Kowalski, K and Mulak, A},
title = {Brain-Gut-Microbiota Axis in Alzheimer's Disease.},
journal = {Journal of neurogastroenterology and motility},
volume = {25},
number = {1},
pages = {48-60},
doi = {10.5056/jnm18087},
pmid = {30646475},
issn = {2093-0879},
abstract = {Disturbances along the brain-gut-microbiota axis may significantly contribute to the pathogenesis of neurodegenerative disorders. Alzheimer's disease (AD) is the most frequent cause of dementia characterized by a progressive decline in cognitive function associated with the formation of amyloid beta (Aβ) plaques and neurofibrillary tangles. Alterations in the gut microbiota composition induce increased permeability of the gut barrier and immune activation leading to systemic inflammation, which in turn may impair the blood-brain barrier and promote neuroinflammation, neural injury, and ultimately neurodegeneration. Recently, Aβ has also been recognized as an antimicrobial peptide participating in the innate immune response. However, in the dysregulated state, Aβ may reveal harmful properties. Importantly, bacterial amyloids through molecular mimicry may elicit cross-seeding of misfolding and induce microglial priming. The Aβ seeding and propagation may occur at different levels of the brain-gut-microbiota axis. The potential mechanisms of amyloid spreading include neuron-to-neuron or distal neuron spreading, direct blood-brain barrier crossing or via other cells as astrocytes, fibroblasts, microglia, and immune system cells. A growing body of experimental and clinical data confirms a key role of gut dysbiosis and gut microbiota-host interactions in neurodegeneration. The convergence of gut-derived inflammatory response together with aging and poor diet in the elderly contribute to the pathogenesis of AD. Modification of the gut microbiota composition by food-based therapy or by probiotic supplementation may create new preventive and therapeutic options in AD.},
}

@article {pmid30646427,
year = {2019},
author = {Zhong, Y and Yang, Y and Liu, P and Xu, R and Rensing, C and Fu, X and Liao, H},
title = {Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.13519},
pmid = {30646427},
issn = {1365-3040},
abstract = {Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines (RILs) contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities, and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes, but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.},
}

@article {pmid30645678,
year = {2019},
author = {Quigley, EMM},
title = {The Spectrum of Small Intestinal Bacterial Overgrowth (SIBO).},
journal = {Current gastroenterology reports},
volume = {21},
number = {1},
pages = {3},
doi = {10.1007/s11894-019-0671-z},
pmid = {30645678},
issn = {1534-312X},
abstract = {PURPOSE OF REVIEW: To critically review recent (past 3 years) literature on the definition, diagnosis, and management of small intestinal bacterial overgrowth (SIBO).

RECENT FINDINGS: While various series continue to illustrate the occurrence of SIBO in disease states where well-known risk factors for its occurrence are present (hypochlorhydria, disorders of intestinal structure or motor function, pancreatic insufficiency, and chronic liver disease, for example), the current challenge is in defining the limits of SIBO. Is SIBO truly common among those with "functional" gastrointestinal symptoms where there is no evidence of maldigestion or malabsorption; the original hallmarks of SIBO? Our attempts to address this question continue to be hampered by the limitations of our diagnostic tool kit. There is hope-the application of modern molecular techniques to the study of the small intestinal microbiome, together with some innovative sampling techniques, such as real-time intestinal gas sampling, may soon allow us to truly define the spectrum of SIBO. SIBO, once removed from its original confines as a cause of malabsorption syndrome, has proven to be an elusive and moving target. Only the most rigorous studies employing validated methodologies will finally corral this mysterious entity.},
}

@article {pmid30644970,
year = {2019},
author = {Kelly, CR and Ananthakrishnan, AN},
title = {Manipulating the Microbiome With Fecal Transplantation to Treat Ulcerative Colitis.},
journal = {JAMA},
volume = {321},
number = {2},
pages = {151-152},
doi = {10.1001/jama.2018.20397},
pmid = {30644970},
issn = {1538-3598},
}

@article {pmid30644566,
year = {2019},
author = {McClanahan, D and Yeh, A and Firek, B and Zettle, S and Rogers, M and Cheek, R and Nguyen, MVL and Gayer, CP and Wendell, SG and Mullett, SJ and Morowitz, MJ},
title = {Pilot Study of the Effect of Plant-Based Enteral Nutrition on the Gut Microbiota in Chronically Ill Tube-Fed Children.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.1504},
pmid = {30644566},
issn = {1941-2444},
abstract = {BACKGROUND: Dietary intake sharply impacts the structure and function of the gut microbiota, which is important for childhood health. However, little is known about the microbiota of children who cannot eat by mouth. Standard enteral formulas for supplemental nutrition are low in fiber and high in processed sugars and are commonly associated with gastrointestinal side effects. In this pilot study, we examined the effects of plant-based enteral nutrition (PBEN) upon the gut bacteria of chronically ill children.

METHODS: Ten children (median age 3.5 years, age range 2-8 years) dependent upon conventional enteral formula were transitioned to PBEN for 2 months. Microbial diversity within fecal samples collected before and after PBEN was assessed by 16S ribosomal RNA gene sequence analysis and was compared with rectal swabs from healthy children. Fecal short-chain fatty acids and bile acids were measured in parallel.

RESULTS: Relative to control samples, fecal samples from study subjects were depleted of commensals (eg, Faecalibacterium) and enriched with pathogens (eg, Enterococcus). Postintervention samples from study subjects were more similar to healthy controls. Most subjects experienced PBEN-induced alterations in the gut microbiota, but these changes varied significantly across individuals. Clinical diaries indicated that PBEN was well tolerated, with improvement in symptoms noted in several subjects.

CONCLUSION: Results from this pilot study suggest that PBEN is well tolerated and could improve the health of the microbiota in chronically ill children. This trial provides a rationale for systematic evaluation of PBEN in clinical trials of children who require supplemental nutrition.},
}

@article {pmid30644442,
year = {2019},
author = {Haron, MH and Tyler, HL and Chandra, S and Moraes, RM and Jackson, CR and Pugh, ND and Pasco, DS},
title = {Plant microbiome-dependent immune enhancing action of Echinacea purpurea is enhanced by soil organic matter content.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {136},
doi = {10.1038/s41598-018-36907-x},
pmid = {30644442},
issn = {2045-2322},
support = {R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {We previously demonstrated that extracts from Echinacea purpurea material varied substantially in their ability to activate macrophages in vitro and that this variation was due to differences in their content of bacterial components. The purpose of the current study was to identify soil conditions (organic matter, nitrogen, and moisture content) that alter the macrophage activation potential of E. purpurea and determine whether these changes in activity correspond to shifts in the plant-associated microbiome. Increased levels of soil organic matter significantly enhanced macrophage activation exhibited by the root extracts of E. purpurea (p < 0.0001). A change in soil organic matter content from 5.6% to 67.4% led to a 4.2-fold increase in the macrophage activation potential of extracts from E. purpurea. Bacterial communities also differed significantly between root materials cultivated in soils with different levels of organic matter (p < 0.001). These results indicate that the level of soil organic matter is an agricultural factor that can alter the bacterial microbiome, and thereby the activity, of E. purpurea roots. Since ingestion of bacterial preparation (e.g., probiotics) is reported to impact human health, it is likely that the medicinal value of Echinacea is influenced by cultivation conditions that alter its associated bacterial community.},
}

@article {pmid30644049,
year = {2019},
author = {Gong, B and Huang, H and Peng, C and Wang, J and Ma, J and Liu, X and Ouyang, S and Huang, SL and Wu, H},
title = {The microbiomic and environmental analysis of sediments in the Indo-Pacific humpback dolphin (Sousa chinensis) habitat in the Northern Beibu Gulf, China.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-018-3976-9},
pmid = {30644049},
issn = {1614-7499},
support = {31560727//National Natural Science Foundation of China/ ; 31570875//National Natural Science Foundation of China/ ; 41776174//National Natural Science Foundation of China/ ; 2014GXNSFBA118135//Guangxi Natural Science Foundation/ ; 2017TS03//Foundation of Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Qinzhou University/ ; 2016ZYB07//Foundation of the Key Laboratory of Coastal Science and Engineering, Beibu Gulf, Guangxi/ ; },
abstract = {The northern Beibu Gulf is one of the major habitats for the Indo-Pacific humpback dolphin (Sousa chinensis) in China. In this habitat, the core distribution zone of humpback dolphins was confined to the Sanniang Bay (SNB) and Dafengjiang River Estuary (DRE) areas. In our present research, the sediments of 14 sampling sites across the SNB and DRE waters were collected and further conducted for microbiomic and environmental analysis to explore the ecosystem characteristics of major humpback dolphin habitats in Northern Beibu Gulf. The environmental condition includes ammonia nitrogen (NH4+-N), nitrate nitrogen (NO3--N), dissolved reactive phosphorus (DRP), sulfur content in the form of sulfuric acid (SO42--S), Fe, and heavy metals (including Cu, Zn, Cd, Pb, and As). The composition of the bacterial community was characterized by 16S ribosomal DNA analysis of the V3-V4 regions using the Illumina-based sequencing platform. The environmental characteristic of the nutrient elements and heavy metals indicated that SNB suffered more anthropogenic impact than DRE. The comparably higher concentration of NH4+-N, NO3--N, DRP, Pb, and Cd in the SNB region was detected. The comparably higher nutrients in the SNB may have resulted in higher biomass and lower dissolved oxygen (DO) profile, which was further proved by Landsat thermal image data. The microbiome analysis showed that the DRE region was oligotrophic and SNB reflected an anaerobic environment in the sediments. Environmental factors rather than the spatial distance determined the similarity of bacterial community among different sites. Ecological associations between environmental, oceanographic, and bacterial characteristics were illustrated, which exhibited strong mutual associations. Our findings presented a feasibility that integrates empirical and remote sensing data to distinguish ecological features and evaluate ecosystem healthiness for the humpback dolphin habitats.},
}

@article {pmid30643883,
year = {2019},
author = {Franco Filho, LC and Barata, RR and Cardoso, JF and Massafra, JMV and Lemos, PDS and Casseb, LMN and Cruz, ACR and Nunes, MRT},
title = {Metagenomic Analysis of Samples from Three Bat Species Collected in the Amazon Rain Forest.},
journal = {Microbiology resource announcements},
volume = {8},
number = {2},
pages = {},
doi = {10.1128/MRA.01422-18},
pmid = {30643883},
issn = {2576-098X},
abstract = {We report here the sequencing of five microbiome samples collected from different bat species in the Amazon rain forest. All contigs matching virus sequences were assigned to members of the Retroviridae family, while the bacterial contigs matched several bacterial species mostly belonging to the Proteobacteria phylum.},
}

@article {pmid30643852,
year = {2019},
author = {Alves da Silva, AV and de Castro Oliveira, SB and Di Rienzi, SC and Brown-Steinke, K and Dehan, LM and Rood, JK and Carreira, VS and Le, H and Maier, EA and Betz, KJ and Aihara, E and Ley, RE and Preidis, GA and Shen, L and Moore, SR},
title = {Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity.},
journal = {Current developments in nutrition},
volume = {3},
number = {1},
pages = {nzy070},
doi = {10.1093/cdn/nzy070},
pmid = {30643852},
issn = {2475-2991},
abstract = {Background: Folate and choline are essential methyl donor nutrients throughout the life span; however, the adverse effects of combined deficiency on early growth, intestinal epithelial morphology, and the gut microbiome remain only partially understood.

Objectives: We investigated the effects of dietary folate and choline deficiency on early growth, small intestinal (SI) epithelial architecture, and the gut microbiota of mice. To explore potential mechanisms for adverse effects on gut epithelial morphology, we also evaluated gene expression and DNA methylation in mouse intestinal epithelial organoids (enteroids) maintained in methyl donor-deficient (MDD) conditions.

Methods: Pregnant dams were administered 1 of 4 diets: 1) control diet (CD-), 2) an isocaloric MDD- diet, or 3) CD+ and 4) MDD+ formulations containing 1% succinylsulfathiazole to inhibit folate-producing gut bacteria. We weaned pups to their dams' diet at 3 wk of age and monitored body weight and tail length pre- and postweaning. We measured serum folate, SI crypt morphology, and microbiota composition at 7 wk of age.

Results: Both MDD+ and MDD- diets impaired early ponderal and linear growth, lowered serum folate concentrations, and produced patchy areas of increased crypt depth throughout the SI. Succinylsulfathiazole increased crypt depth independently of diet. MDD or succinylsulfathiazole, alone or in combination, altered the gut microbiome, with decreased Bacteroidales and Clostridiales, increased Lactobacillales and Erysipelotrichaceae taxa, and decreased α-diversity indexes. Enteroids maintained in MDD media displayed dysmorphic crypt domains, altered expression of stem cell and secretory differentiation genes, and decreased DNA methylation of the glycosylation genes Beta-1,4-N-Acetyl-Galactosaminyltransferase-1 (B4galnt1) and Phosphoethanolamine/Phosphocholine-Phosphatase (Phospho1).

Conclusion: MDD impairs ponderal and linear growth in mice in association with dysmorphic SI crypts and reduced gut microbial diversity. In vitro methyl donor deficiency similarly induced dysmorphic crypts in mouse enteroids in conjunction with altered gene expression and DNA methylation.},
}

@article {pmid30643689,
year = {2019},
author = {Kirchoff, NS and Udell, MAR and Sharpton, TJ},
title = {The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris).},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6103},
doi = {10.7717/peerj.6103},
pmid = {30643689},
issn = {2167-8359},
abstract = {Aggression is a serious behavioral disorder in domestic dogs that endangers both dogs and humans. The underlying causes of canine aggression are poorly resolved and require illumination to ensure effective therapy. Recent research links the compositional diversity of the gut microbiome to behavioral and psychological regulation in other mammals, such as mice and humans. Given these observations, we hypothesized that the composition of the canine gut microbiome could associate with aggression. We analyzed fecal microbiome samples collected from a small population of pit bull type dogs seized from a dogfighting organization. This population included 21 dogs that displayed conspecific aggressive behaviors and 10 that did not. Beta-diversity analyses support an association between gut microbiome structure and dog aggression. Additionally, we used a phylogenetic approach to resolve specific clades of gut bacteria that stratify aggressive and non-aggressive dogs, including clades within Lactobacillus, Dorea, Blautia, Turicibacter, and Bacteroides. Several of these taxa have been implicated in modulating mammalian behavior as well as gastrointestinal disease states. Although sample size limits this study, our findings indicate that gut microorganisms are linked to dog aggression and point to an aggression-associated physiological state that interacts with the gut microbiome. These results also indicate that the gut microbiome may be useful for diagnosing aggressive behaviors prior to their manifestation and potentially discerning cryptic etiologies of aggression.},
}

@article {pmid30643680,
year = {2019},
author = {Duguma, D and Hall, MW and Smartt, CT and Debboun, M and Neufeld, JD},
title = {Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6168},
doi = {10.7717/peerj.6168},
pmid = {30643680},
issn = {2167-8359},
abstract = {Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.},
}

@article {pmid30643213,
year = {2019},
author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH},
title = {Metagenomic engineering of the mammalian gut microbiome in situ.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-018-0301-y},
pmid = {30643213},
issn = {1548-7105},
abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.},
}

@article {pmid30642603,
year = {2019},
author = {Chermprapai, S and Ederveen, THA and Broere, F and Broens, EM and Schlotter, YM and van Schalkwijk, S and Boekhorst, J and van Hijum, SAFT and Rutten, VPMG},
title = {The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study.},
journal = {Veterinary microbiology},
volume = {229},
number = {},
pages = {90-99},
doi = {10.1016/j.vetmic.2018.12.022},
pmid = {30642603},
issn = {1873-2542},
abstract = {Canine atopic dermatitis is a genetically predisposed inflammatory and pruritic allergic skin disease that is often complicated by (secondary) bacterial and fungal (yeast) infections. High-throughput DNA sequencing was used to characterize the composition of the microbiome (bacteria and fungi) inhabiting specific sites of skin in healthy dogs and dogs with atopic dermatitis (AD) before and after topical antimicrobial treatment. Skin microbiome samples were collected from six healthy control dogs and three dogs spontaneously affected by AD by swabbing at (non-) predilection sites before, during and after treatment. Bacteria and fungi were profiled by Illumina sequencing of the 16S ribosomal RNA gene of bacteria (16S) and the internally transcribed spacer of the ribosomal gene cassette in fungi (ITS). The total cohort of dogs showed a high diversity of microbes on skin with a strong individual variability of both 16S and ITS profiles. The genera of Staphylococcus and Porphyromonas were dominantly present both on atopic and healthy skin and across all skin sites studied. In addition, bacterial and fungal alpha diversity were similar at the different skin sites. The topical antimicrobial treatment increased the diversity of bacterial and fungal compositions in course of time on both AD and healthy skin.},
}

@article {pmid30642560,
year = {2019},
author = {de Nonneville, A},
title = {[Gut microbiome influences efficacy of immunotherapy].},
journal = {Bulletin du cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bulcan.2018.12.004},
pmid = {30642560},
issn = {1769-6917},
}

@article {pmid30642394,
year = {2019},
author = {Hitschfeld, M and Tovar, E and Gupta, S and Bik, EM and Palmer, C and Hoaglin, MC and Almonacid, DE and Richman, J and Apte, ZS},
title = {The role of a sequencing-based clinical intestinal screening test in patients at high-risk for Clostridium difficile and other pathogens: a case report.},
journal = {Journal of medical case reports},
volume = {13},
number = {1},
pages = {9},
doi = {10.1186/s13256-018-1919-1},
pmid = {30642394},
issn = {1752-1947},
abstract = {BACKGROUND: Hospitalization and antibiotic treatment can put patients at high risk for Clostridium difficile infection, where a disturbance of the gut microbiome allows for Clostridium difficile proliferation and associated symptoms, including mild, moderate, or severe diarrhea. Clostridium difficile infection is challenging to treat, often recurrent, and leads to almost 30,000 annual deaths in the USA alone. Here we present a case where SmartGut™, an at-home, self-administered sequencing-based clinical intestinal screening test, was used to identify the presence of Clostridium difficile in a patient with worsening diarrhea. Identification of this pathogen and subsequent treatment led to a significant improvement in symptoms.

CASE PRESENTATION: The patient is a 29-year-old white woman with a history of severe irritable bowel syndrome with diarrhea, hemorrhoidectomy, and anal sphincterotomy complicated by a perianal fistula and perirectal abscesses that required extended courses of broad-spectrum antibiotics. In June 2016, she developed intermittent Clostridium difficile infections, which required continued antibiotic use. Months later she used an at-home, self-administered, intestinal microbial test, the first of which was negative for the presence of Clostridium difficile, but it detected the relative abundance of microbes associated with irritable bowel syndrome outside the healthy reference ranges. In the subsequent 2 months after the negative Clostridium difficile result, her gastrointestinal symptoms worsened dramatically. A second microbiome test resulted in a positive Clostridium difficile finding and continued abnormal microbial parameters, which led the treating physician to refer her to a gastroenterologist. Additional testing confirmed the presence of Clostridium difficile with a toxin-positive strain. She received treatment immediately and her gastrointestinal symptoms improved significantly over the next week.

CONCLUSIONS: This case report suggests that more frequent DNA testing for Clostridium difficile infections may be indicated in patients that are at high-risk for Clostridium difficile infection, especially for patients with irritable bowel syndrome, and those who undergo gastrointestinal surgery and/or an extended antibiotic treatment. This report also shows that such testing could be effectively performed using at-home, self-administered sequencing-based clinical intestinal microbial screening tests. Further research is needed to investigate whether the observations reported here extrapolate to a larger cohort of patients.},
}

@article {pmid30642389,
year = {2019},
author = {Li, F and Hitch, TCA and Chen, Y and Creevey, CJ and Guan, LL},
title = {Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {6},
doi = {10.1186/s40168-019-0618-5},
pmid = {30642389},
issn = {2049-2618},
support = {BB/E/W/10964A01 and BBS/OS/GC/000011B//BBSRC/ ; 2013R029R//Alberta Livestock and Meat Agency/ ; 2015P008R//Alberta Livestock and Meat Agency/ ; Discovery//Natural Sciences and Engineering Research Council of Canada/ ; Doctoral Scholarship//Alberta Innovates - Technology Futures/ ; Scholarship//GPLER/ ; },
abstract = {BACKGROUND: Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.

RESULTS: Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.

CONCLUSIONS: Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.},
}

@article {pmid30642327,
year = {2019},
author = {Hurley, E and Barrett, MPJ and Kinirons, M and Whelton, H and Ryan, CA and Stanton, C and Harris, HMB and O'Toole, PW},
title = {Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children.},
journal = {BMC oral health},
volume = {19},
number = {1},
pages = {13},
doi = {10.1186/s12903-018-0693-1},
pmid = {30642327},
issn = {1472-6831},
abstract = {BACKGROUND: The main objectives of this study were to describe and compare the microbiota of 1) deep dentinal lesions of deciduous teeth of children affected with severe early childhood caries (S-ECC) and 2) the unstimulated saliva of these children and 3) the unstimulated saliva of caries-free children, and to compare microbiota compositional differences and diversity of taxa in these sampled sites.

METHODS: Children with S-ECC and without S-ECC were recruited. The saliva of all children with and without S-ECC was sampled along with the deep dentinal microbiota from children affected by S-ECC. The salivary microbiota of children affected by S-ECC (n = 68) was compared to that of caries-free children (n = 70), by Illumina MiSeq sequencing of 16S rRNA amplicons. Finally, the caries microbiota of deep dentinal lesions of those children with S-ECC was investigated.

RESULTS: Using two beta diversity metrics (Bray Curtis dissimilarity and UniFrac distance), the caries microbiota was found to be distinct from that of either of the saliva groups (caries-free & caries-active) when bacterial abundance was taken into account. However, when the comparison was made by measuring only presence and absence of bacterial taxa, all three microbiota types separated. While the alpha diversity of the caries microbiota was lowest, the diversity difference between the caries samples and saliva samples was statistically significant (p < 0.001). The major phyla of the caries active dentinal microbiota were Firmicutes (median abundance value 33.5%) and Bacteroidetes (23.2%), with Neisseria (10.3%) being the most abundant genus, followed by Prevotella (10%). The caries-active salivary microbiota was dominated by Proteobacteria (median abundance value 38.2%) and Bacteroidetes (27.8%) with the most abundant genus being Neisseria (16.3%), followed by Porphyromonas (9.5%). Caries microbiota samples were characterized by high relative abundance of Streptococcus mutans, Prevotella spp., Bifidobacterium and Scardovia spp.

CONCLUSIONS: Distinct differences between the caries microbiota and saliva microbiota were identified, with separation of both salivary groups (caries-active and caries-free) whereby rare taxa were highlighted. While the caries microbiota was less diverse than the salivary microbiota, the presence of these rare taxa could be the difference between health and disease in these children.},
}

@article {pmid30642207,
year = {2019},
author = {Emerson, D},
title = {The role of iron-oxidizing bacteria in biocorrosion: a review.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/08927014.2018.1526281},
pmid = {30642207},
issn = {1029-2454},
abstract = {Lithotrophic iron-oxidizing bacteria depend on reduced iron, Fe(II), as their primary energy source, making them natural candidates for growing in association with steel infrastructure and potentially contributing to microbially influenced corrosion (MIC). This review summarizes recent work on the role of iron-oxidizing bacteria (FeOB) in MIC. By virtue of producing complex 3-dimensional biofilms that result from the accumulation of iron-oxides, FeOB may aid in the colonization of steel surfaces by other microbes involved in MIC. Evidence points to a successional pattern occurring whereby FeOB are early colonizers of mild steel (MS), followed by sulfate-reducing bacteria and other microbes, although studies of aged corrosion products indicate that FeOB do establish a long-term presence. There is evidence that only specific clades of FeOB, with unique adaptations for growing on steel surfaces are part of the MIC community. These are discussed in the context of the larger MIC microbiome.},
}

@article {pmid30642052,
year = {2019},
author = {Niccolai, E and Boem, F and Russo, E and Amedei, A},
title = {The Gut⁻Brain Axis in the Neuropsychological Disease Model of Obesity: A Classical Movie Revised by the Emerging Director "Microbiome".},
journal = {Nutrients},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/nu11010156},
pmid = {30642052},
issn = {2072-6643},
support = {Prot. n°2018.005//Fondazione Cassa di Risparmio Pistoia e Pescia/ ; Programma Attuativo Regionale Toscana funded by FAS - MICpROBIMM//Regione Toscana/ ; },
abstract = {The worldwide epidemic of obesity has become an important public health issue, with serious psychological and social consequences. Obesity is a multifactorial disorder in which various elements (genetic, host, and environment), play a definite role, even if none of them satisfactorily explains its etiology. A number of neurological comorbidities, such as anxiety and depression, charges the global obesity burden, and evidence suggests the hypothesis that the brain could be the seat of the initial malfunction leading to obesity. The gut microbiome plays an important role in energy homeostasis regulating energy harvesting, fat deposition, as well as feeding behavior and appetite. Dietary patterns, like the Western diet, are known to be a major cause of the obesity epidemic, probably promoting a dysbiotic drift in the gut microbiota. Moreover, the existence of a "gut⁻brain axis" suggests a role for microbiome on hosts' behavior according to different modalities, including interaction through the nervous system, and mutual crosstalk with the immune and the endocrine systems. In the perspective of obesity as a real neuropsychological disease and in light of the discussed considerations, this review focuses on the microbiome role as an emerging director in the development of obesity.},
}

@article {pmid30642013,
year = {2019},
author = {Gianchecchi, E and Fierabracci, A},
title = {Recent Advances on Microbiota Involvement in the Pathogenesis of Autoimmunity.},
journal = {International journal of molecular sciences},
volume = {20},
number = {2},
pages = {},
doi = {10.3390/ijms20020283},
pmid = {30642013},
issn = {1422-0067},
support = {Ricerca Corrente 201802P004265//Ministero della Salute/ ; },
abstract = {Autoimmune disorders derive from genetic, stochastic, and environmental factors that all together interact in genetically predisposed individuals. The impact of an imbalanced gut microbiome in the pathogenesis of autoimmunity has been suggested by an increasing amount of experimental evidence, both in animal models and humans. Several physiological mechanisms, including the establishment of immune homeostasis, are influenced by commensal microbiota in the gut. An altered microbiota composition produces effects in the gut immune system, including defective tolerance to food antigens, intestinal inflammation, and enhanced gut permeability. In particular, early findings reported differences in the intestinal microbiome of subjects affected by several autoimmune conditions, including prediabetes or overt disease compared to healthy individuals. The present review focuses on microbiota-host homeostasis, its alterations, factors that influence its composition, and putative involvement in the development of autoimmune disorders. In the light of the existing literature, future studies are necessary to clarify the role played by microbiota modifications in the processes that cause enhanced gut permeability and molecular mechanisms responsible for autoimmunity onset.},
}

@article {pmid30641975,
year = {2019},
author = {Bowyer, RCE and Jackson, MA and Le Roy, CI and Ni Lochlainn, M and Spector, TD and Dowd, JB and Steves, CJ},
title = {Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study.},
journal = {Microorganisms},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/microorganisms7010017},
pmid = {30641975},
issn = {2076-2607},
support = {WT081878MA//Wellcome Trust/United Kingdom ; R21 AI21784-01//National Institutes of Health/ ; },
abstract = {Socioeconomic inequalities in health and mortality are well established, but the biological mechanisms underlying these associations are less understood. In parallel, the gut microbiome is emerging as a potentially important determinant of human health, but little is known about its broader environmental and social determinants. We test the association between gut microbiota composition and individual- and area-level socioeconomic factors in a well-characterized twin cohort. In this study, 1672 healthy volunteers from twin registry TwinsUK had data available for at least one socioeconomic measure, existing fecal 16S rRNA microbiota data, and all considered co-variables. Associations with socioeconomic status (SES) were robust to adjustment for known health correlates of the microbiome; conversely, these health-microbiome associations partially attenuated with adjustment for SES. Twins discordant for IMD (Index of Multiple Deprivation) were shown to significantly differ by measures of compositional dissimilarity, with suggestion the greater the difference in twin pair IMD, the greater the dissimilarity of their microbiota. Future research should explore how SES might influence the composition of the gut microbiota and its potential role as a mediator of differences associated with SES.},
}

@article {pmid30641967,
year = {2019},
author = {Yoon, WJ and Kim, HN and Park, E and Ryu, S and Chang, Y and Shin, H and Kim, HL and Yi, SY},
title = {The Impact of Cholecystectomy on the Gut Microbiota: A Case-Control Study.},
journal = {Journal of clinical medicine},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/jcm8010079},
pmid = {30641967},
issn = {2077-0383},
support = {NRF-2018R1D1A1B07-050067//National Research Foundation of Korea/ ; 2-2018-0257-001-1//Pharmbio Korea Co., Ltd./ ; },
abstract = {Cholecystectomy alters the bile flow into the intestine and the enterohepatic circulation of the bile acids; this may affect the gut microbiota. We assessed the gut microbiota composition of patients who had undergone cholecystectomy and compared with those who had not. From a cohort of 1463 adult participants who underwent comprehensive health screening examinations, 27 subjects who had undergone cholecystectomy (cholecystectomy group) and 81 age- and sex-matched subjects who had not (control group) were selected. Clinical parameters were collected and compared. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from fecal samples. We evaluated differences in the overall microbial composition and in the abundance of taxa. The two groups were comparable with respect to clinical characteristics and laboratory results. The actual number of taxa observed in a sample (observed features) was significantly lower in the cholecystectomy group than in the control group (p = 0.042). The beta diversity of Jaccard distance index was significantly different between the two groups (p = 0.027). Blautia obeum and Veillonella parvula were more abundant in the cholecystectomy group. The difference in the diversity of the gut microbiota between the cholecystectomy and control groups was subtle. However, B. obeum and V. parvula, which have azoreductase activity, were more abundant in the cholecystectomy group. The impact of such changes in the gut microbiota on health remains to be determined.},
}

@article {pmid30641869,
year = {2019},
author = {Torcia, MG},
title = {Interplay among Vaginal Microbiome, Immune Response and Sexually Transmitted Viral Infections.},
journal = {International journal of molecular sciences},
volume = {20},
number = {2},
pages = {},
doi = {10.3390/ijms20020266},
pmid = {30641869},
issn = {1422-0067},
support = {62042012//Regione Toscana/ ; -//Istituto Toscano Tumori/ ; -//Ente Cassa di Risparmio di Firenze/ ; },
abstract = {The vaginal ecosystem is important for women's health and for a successful reproductive life, and an optimal host-microbial interaction is required for the maintenance of eubiosis. The vaginal microbiota is dominated by Lactobacillus species in the majority of women. Loss of Lactobacillus dominance promotes the colonization by anaerobic bacterial species with an increase in microbial diversity. Vaginal dysbiosis is a very frequent condition which affects the immune homeostasis, inducing a rupture in the epithelial barrier and favoring infection by sexually transmitted pathogens. In this review, we describe the known interactions among immune cells and microbial commensals which govern health or disease status. Particular attention is given to microbiota compositions which, through interplay with immune cells, facilitate the establishment of viral infections, such as Human Immunodeficiency Virus (HIV), Human Papilloma Virus (HPV), Herpes Simplex Virus 2 (HSV2).},
}

@article {pmid30640865,
year = {2018},
author = {Schnapp, Z and Hartman, C and Livnat, G and Shteinberg, M and Elenberg, Y},
title = {Decreased Fecal Calprotectin Levels in Cystic Fibrosis Patients After Antibiotic Treatment for Respiratory Exacerbation.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002197},
pmid = {30640865},
issn = {1536-4801},
abstract = {OBJECTIVES: In all patients with cystic fibrosis (CF), gastrointestinal (GI) tract cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction occurs early in life. .The identical pathophysiological triad of obstruction, infection and inflammation causes disease of the airways and in the intestinal tract (CF enteropathy). Mucus accumulation within GI tract is a niche for abnormal microbial colonization, leading to dysbiosis. Fecal calprotectin (FC) is a neutrophil cytosolic protein released during apoptosis and necrosis and reflects inflammatory status. Systemic antibiotic treatment for pulmonary exacerbations has been shown to improve systemic inflammatory markers as well as serum and sputum calprotectin. Antibiotic treatment aimed at pulmonary complaints may improve GI tract inflammatory status. We hypothesized that high levels of fecal calprotectin present during pulmonary exacerbation are due, in part, to multi-organ dysbiosis and thus should diminish with systemic antibiotic treatment.

METHODS: This prospective pilot study enrolled 14 patients with CF, with no current GI symptoms. FC levels and lung function were measured at the beginning and end of systemic antibiotic treatment.

RESULTS: Compared to pre-antibiotic treatment baseline values, end of treatment FC levels declined significantly after antibiotic treatment, P = 0.004 and similarly, there was significant improvement in FEV1.0, P = 0.002.

CONCLUSIONS: High levels of FC during respiratory exacerbation may reflect a systemic exacerbation rather than solely pulmonary. Antibiotic treatment lowered the FC levels possibly by its impact on the intestinal microbiome.},
}

@article {pmid30640740,
year = {2019},
author = {Polsinelli, VB and Marteau, L and Shah, SJ},
title = {The role of splanchnic congestion and the intestinal microenvironment in the pathogenesis of advanced heart failure.},
journal = {Current opinion in supportive and palliative care},
volume = {},
number = {},
pages = {},
doi = {10.1097/SPC.0000000000000414},
pmid = {30640740},
issn = {1751-4266},
abstract = {PURPOSE OF REVIEW: Right-sided heart failure, which is often present in the setting of advanced heart failure, is associated with cardiac cachexia, the cardiorenal syndrome, and adverse outcomes. Improved understanding of venous congestion of the splanchnic circulation, which may play a key role in the pathogenesis of right-sided heart failure, could lead to novel therapeutics to ameliorate heart failure. Here we provide an overview of right-sided heart failure, splanchnic hemodynamics, fluid homeostasis, and the intestinal microenvironment. We review recent literature to describe pathophysiologic mechanisms and possible therapeutics.

RECENT FINDINGS: Several possible mechanisms centered around upregulation of sodium-hydrogen exchanger-3 (NHE3) may form a causal link between right ventricular dysfunction, splanchnic congestion, and worsening heart failure. These include an anaerobic environment in enterocytes, resulting in reduced intracellular pH; increased sodium absorption by the gut via NHE3; decreased pH at the intestinal brush border thus altering the gut microbiome profile; increased bacterial synthesis of trimethylamine N-oxide; and decreased bacterial synthesis of short-chain fatty acids causing abnormal intestinal barrier function.

SUMMARY: Splanchnic congestion in the setting of right-sided heart failure may serve an important role in the pathogenesis of advanced heart failure, and further exploration of these mechanisms may lead to new therapeutic advances.},
}

@article {pmid30640680,
year = {2019},
author = {Chao, XP and Sun, TT and Wang, S and Fan, QB and Shi, HH and Zhu, L and Lang, JH},
title = {Correlation between the diversity of vaginal microbiota and the risk of high-risk human papillomavirus infection.},
journal = {International journal of gynecological cancer : official journal of the International Gynecological Cancer Society},
volume = {29},
number = {1},
pages = {28-34},
doi = {10.1136/ijgc-2018-000032},
pmid = {30640680},
issn = {1525-1438},
abstract = {OBJECTIVES: Since other genital infections enhance HIV susceptibility by inducing inflammation and evidence suggests that the vaginal microbiome plays a functional role in the persistence or regression of high-risk human papillomavirus (HPV) infections, we investigated the relationship between the composition of the vaginal microbiota and the risk of high-risk HPV infection.

METHODS: The study included 151 healthy women (65 HPV-positive and 86 HPV-negative) aged 20-65 at enrollment. Total genome DNA from samples was extracted using the hexadecyltrimethylammonium bromide (CTAB) CTAB method. The vaginal microbiota composition was determined by sequencing barcoded 16S rDNA gene fragments (V4) on Illumina HiSeq2500.

RESULTS: Of the 30 most abundant bacteria at the genus level, we found only six bacteria with a statistical difference between HPV-positive and HPV-negative women: Bacteroides, Acinetobacter, Faecalibacterium, Streptococcus, Finegoldia, and Moryella. Lactobacillus was the predominant genus and was detected in all women, but there was no significant difference between the two groups for L. iners, L. jensenii, and L. gasseri. Furthermore, we found 26 types of bacteria with a statistical difference at the species level between the two groups. Anaerobic bacteria such as Bacteroides plebeius, Acinetobacter lwoffii, and Prevotella buccae were found significantly more frequently in HPV-positive women, which is the most important finding of our study.

CONCLUSION: Our findings suggest a possible role for the composition of the vaginal microbiota as a modifier of high-risk HPV infection, and specific microbiota species may serve as sensors for changes in the cervical microenvironment associated with high-risk HPV infection. The exact molecular mechanism of the vaginal microbiota in the course of high-risk HPV infection and cervical neoplasia should be further explored. Future research should include intervention in the composition of the vaginal microbiota to reverse the course of high-risk HPV infection and the natural history of cervical neoplasia.},
}

@article {pmid30640553,
year = {2019},
author = {Ozkan, J and Willcox, MD},
title = {The Ocular Microbiome: Molecular Characterization of a Unique and Low Microbial Environment.},
journal = {Current eye research},
volume = {},
number = {},
pages = {},
doi = {10.1080/02713683.2019.1570526},
pmid = {30640553},
issn = {1460-2202},
abstract = {The ocular surface is continually exposed to bacteria from the environment and traditional culture-based microbiological studies have isolated a low diversity of microorganisms from this region. The use of culture-independent methods to define the ocular microbiome, primarily involving 16S ribosomal RNA gene sequencing, has shown that the microbial communities present on the ocular surface have a greater diversity than previously reported and appear to have an immune modulating function. These molecular techniques have been used to investigate the effect of contact lens wear and disease on the microbiota of the ocular surface and eyelids and these studies have consistently identified bacteria not previously identified in normal eyes. Recent studies also suggest a role of the ocular and non-ocular microbiome in retinal disease including age-related macular degeneration, glaucoma, uveitis and diabetic retinopathy. However, issues remain regarding the impact of contamination in these culture-independent sequencing techniques, particularly when investigating low microbial biomass samples from the eye. Ocular microbiome studies need to recognise the potential for contamination to impact findings and carefully control each stage of the experimental procedure and to utilise statistical methods to identify contamination signals.},
}

@article {pmid30639436,
year = {2019},
author = {Leung, DYM},
title = {The Microbiome and Allergic Diseases: A struggle between good and bad microbes.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2019.01.003},
pmid = {30639436},
issn = {1534-4436},
}

@article {pmid30639376,
year = {2019},
author = {Ferreira Felizardo, RJ and Mizuno Watanabe, IK and Dardi, P and Venturini Rossoni, L and Olsen Saraiva Câmara, N},
title = {The interplay among gut microbiota, hypertension and kidney diseases: the role of short-chain fatty acids.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.phrs.2019.01.019},
pmid = {30639376},
issn = {1096-1186},
abstract = {The bacteria community living in the gut maintains a symbiotic relationship with the host and its unbalance has been associated with progression of a wide range of intestinal and extra intestinal conditions. Hypertension and chronic kidney disease (CKD) are closely associated diseases with high incidence rates all over the world. Increasing data have supported the involvement of gut microbiome in the blood pressure regulation and the impairment of CKD prognosis. In hypertension, the reduced number of short-chain fatty acids (SCFAs) producing bacteria is associated with modifications in gut environment, involving reduction of the hypoxic gut profile and worsening of the microbial balance, leading to a loss of epithelial barrier integrity, development of gut inflammation and the reduction of SCFAs plasma levels. Those modifications compromise the blood pressure regulation and, as a consequence, favor the end organ damage, also affecting the kidneys. In CKD, impaired renal function leads to accumulation of high levels of uremic toxins that reach the intestine and cause alterations in bacteria composition and fecal metabolite profile, inducing a positive feedback that allows translocation of endotoxins into the bloodstream, which enhances local kidney inflammation and exacerbate kidney injury, compromising even more CKD prognosis. In line with these data, the use of prebiotics, probiotics and fecal microbiota transplantation are becoming efficient therapies to improve the gut dysbiosis aiming hypertension and CKD treatment. This review describes how changes in gut microbiota composition can affect the development of hypertension and the progression of kidney diseases, highlighting the importance of the gut microbial composition uncovering to improve human health maintenance and, especially, for the development of new alternative therapies.},
}

@article {pmid30639346,
year = {2019},
author = {Davidson, WF and Leung, DYM and Beck, LA and Berin, CM and Boguniewicz, M and Busse, WW and Chatila, TA and Geha, RS and Gern, JE and Guttman-Yassky, E and Irvine, AD and Kim, BS and Kong, HH and Lack, G and Nadeau, KC and Schwaninger, J and Simpson, A and Simpson, EL and Spergel, JM and Togias, A and Wahn, U and Wood, RA and Woodfolk, JA and Ziegler, SF and Plaut, M},
title = {Report from the National Institute of Allergy and Infectious Diseases Workshop on "Atopic Dermatitis and the Atopic March: Mechanisms and Interventions".},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2019.01.003},
pmid = {30639346},
issn = {1097-6825},
abstract = {Atopic dermatitis (AD) affects up to 20% of children world-wide and is an increasing public health problem particularly in developed countries. Although AD in infants and young children can resolve, there is a well-recognized, increased risk of sequential progression from AD to other atopic diseases including food allergy, allergic rhinitis, allergic asthma and allergic rhinoconjunctivitis; a process referred to as the "atopic march". The mechanisms underlying the development of AD and subsequent progression to other atopic comorbidities, particularly food allergy, are incompletely understood and the subject of intense investigation. Other major research objectives are the development of effective strategies to prevent AD and food allergy as well as therapeutic interventions to inhibit the atopic march. In 2017, the Division of Allergy, Immunology and Transplantation of the National Institute of Allergy and Infectious Diseases sponsored a workshop to discuss current understanding and important advances in these research areas and to identify gaps in knowledge and future research directions. International and national experts in the field were joined by representatives from several National Institutes of Health institutes. Summaries of workshop presentations, key conclusions and recommendations are presented herein.},
}

@article {pmid30638679,
year = {2018},
author = {Langan, D and Kim, EY and Moudgil, KD},
title = {Modulation of autoimmune arthritis by environmental 'hygiene' and commensal microbiota.},
journal = {Cellular immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cellimm.2018.12.005},
pmid = {30638679},
issn = {1090-2163},
abstract = {Observations in patients with autoimmune diseases and studies in animal models of autoimmunity have revealed that external environmental factors including exposure to microbes and the state of the host gut microbiota can influence susceptibility to autoimmunity and subsequent disease development. Mechanisms underlying these outcomes continue to be elucidated. These include deviation of the cytokine response and imbalance between pathogenic versus regulatory T cell subsets. Furthermore, specific commensal organisms are associated with enhanced severity of arthritis in susceptible individuals, while exposure to certain microbes or helminths can afford protection against this disease. In addition, the role of metabolites (e.g., short-chain fatty acids, tryptophan catabolites), produced either by the microbes themselves or from their action on dietary products, in modulation of arthritis is increasingly being realized. In this context, re-setting of the microbial dysbiosis in RA using prebiotics, probiotics, or fecal microbial transplant is emerging as a promising approach for the prevention and treatment of arthritis. It is hoped that advances in defining the interplay between gut microbiota, dietary products, and bioactive metabolites would help in the development of therapeutic regimen customized for the needs of individual patients in the near future.},
}

@article {pmid30638398,
year = {2019},
author = {Kara, SS and Volkan, B and Erten, I},
title = {Lactobacillus rhamnosus GG can protect malnourished children.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-8},
doi = {10.3920/BM2018.0071},
pmid = {30638398},
issn = {1876-2891},
abstract = {Malnutrition affects virtually all organ systems, and malnourished children are more prone to infections. These children have dysbiosis, but probiotics can restore the disrupted gut microbiome. We investigated the protective effects of Lactobacillus rhamnosus GG in malnourished children in terms of incidence of infection, and anthropometric and metabolic parameters. 50 intervention and 50 control patients, aged 6 months to 5 years, with body weight and height below -2 SD, were randomly and prospectively recruited. The controls received a calorie and protein-appropriate diet for 3 months, while the study group additionally received approximately 109 L. rhamnosus GG for 3 months. Infection episodes and nutritional status were compared between the groups. 38 intervention, 33 control patients completed the study and the two groups were similar at baseline. The study group had fewer upper respiratory tract infections and gastroenteritis episodes at each month and at the end of the study. Children in the study group experienced fewer total upper respiratory infections and urinary tract infections. Hospitalisation was more frequent in the control group during the third month and at the end of the study. Total infection numbers were higher in the control group at each month and at the end of the study (P<0.001 for each). Increments in body mass index (BMI) and BMI Z-scores were more pronounced in the study group (P=0.008 and P=0.02, respectively). Daily prophylactic use of L. rhamnosus GG at 109 bacteria in malnourished children prevents most infections and improves nutritional status when used together with appropriate diet.},
}

@article {pmid30637962,
year = {2019},
author = {Asante, J and Osei Sekyere, J},
title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12735},
pmid = {30637962},
issn = {1758-2229},
abstract = {Our inability to cultivate most micro-organisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and non-living environments. As a result, reservoirs, sources, and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics, and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs, and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning, and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes. This article is protected by copyright. All rights reserved.},
}

@article {pmid30637938,
year = {2019},
author = {Gotoh, A and Ojima, MN and Katayama, T},
title = {Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13366},
pmid = {30637938},
issn = {1751-7915},
support = {17J08530//JSPS Research Fellows/ ; 15H04481 and 17K19231//JSPS-KAKENHI/ ; //Institute for Fermentation/ ; },
abstract = {The human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA-based taxonomic analyses using next-generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 1013 microbial cells, NGS read counts are given in multiples of 106 , making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as 'keystone species', which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host-derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO-mediated microbiota formation in the infant gut.},
}

@article {pmid30637341,
year = {2019},
author = {Blaustein, RA and McFarland, AG and Ben Maamar, S and Lopez, A and Castro-Wallace, S and Hartmann, EM},
title = {Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil.},
journal = {mSystems},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/mSystems.00281-18},
pmid = {30637341},
issn = {2379-5077},
abstract = {Understanding underlying mechanisms involved in microbial persistence in the built environment (BE) is essential for strategically mitigating potential health risks. To test the hypothesis that BEs impose selective pressures resulting in characteristic adaptive responses, we performed a pangenomics meta-analysis leveraging 189 genomes (accessed from GenBank) of two epidemiologically important taxa, Bacillus cereus and Staphylococcus aureus, isolated from various origins: the International Space Station (ISS; a model BE), Earth-based BEs, soil, and humans. Our objectives were to (i) identify differences in the pangenomic composition of generalist and host-associated organisms, (ii) characterize genes and functions involved in BE-associated selection, and (iii) identify genomic signatures of ISS-derived strains of potential relevance for astronaut health. The pangenome of B. cereus was more expansive than that of S. aureus, which had a dominant core component. Genomic contents of both taxa significantly correlated with isolate origin, demonstrating an importance for biogeography and potential niche adaptations. ISS/BE-enriched functions were often involved in biosynthesis, catabolism, materials transport, metabolism, and stress response. Multiple origin-enriched functions also overlapped across taxa, suggesting conserved adaptive processes. We further characterized two mobile genetic elements with local neighborhood genes encoding biosynthesis and stress response functions that distinctively associated with B. cereus from the ISS. Although antibiotic resistance genes were present in ISS/BE isolates, they were also common in counterparts elsewhere. Overall, despite differences in microbial lifestyle, some functions appear common to remaining viable in the BE, and those functions are not typically associated with direct impacts on human health. IMPORTANCE The built environment contains a variety of microorganisms, some of which pose critical human health risks (e.g., hospital-acquired infection, antibiotic resistance dissemination). We uncovered a combination of complex biological functions that may play a role in bacterial survival under the presumed selective pressures in a model built environment-the International Space Station-by using an approach to compare pangenomes of bacterial strains from two clinically relevant species (B. cereus and S. aureus) isolated from both built environments and humans. Our findings suggest that the most crucial bacterial functions involved in this potential adaptive response are specific to bacterial lifestyle and do not appear to have direct impacts on human health.},
}

@article {pmid30637338,
year = {2018},
author = {Bai, Y and Tao, J and Zhou, J and Fan, Q and Liu, M and Hu, Y and Xu, Y and Zhang, L and Yuan, J and Li, W and Ze, X and Malard, P and Guo, Z and Yan, J and Li, M},
title = {Fucosylated Human Milk Oligosaccharides and N-Glycans in the Milk of Chinese Mothers Regulate the Gut Microbiome of Their Breast-Fed Infants during Different Lactation Stages.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00206-18},
pmid = {30637338},
issn = {2379-5077},
abstract = {The milk glycobiome has a significant impact on the gut microbiota of infants, which plays a pivotal role in health and development. Fucosylated human milk oligosaccharides (HMOs) and N-glycans on milk proteins are beneficial for the development of healthy gut microbiota, and the fucosylation levels of these glycans can be affected by the maternal fucosyltransferase 2 gene (FUT2). Here, we present results of longitudinal research on paired milk and stool samples from 56 Chinese mothers (CMs) and their breast-fed children. Changes of HMOs and fucosylated N-glycans in milk of CMs at different lactation stages were detected, which allowed characterization of the major differences in milk glycans and consequential effects on the gut microbiome of infants according to maternal FUT2 status. Significant differences in the abundance of total and fucosylated HMOs between secretor and nonsecretor CMs were noted, especially during early lactation. Despite a tendency toward decreasing milk protein concentrations, the fucosylation levels of milk N-glycans increased during late lactation. The changes in the levels of fucosylated HMOs and milk N-glycans were highly correlated with the growth of Bifidobacterium spp. and Lactobacillus spp. in the gut of infants during early and later lactation, respectively. Enriched expression of genes encoding glycoside hydrolases, glycosyl transferases, ATP-binding cassette (ABC) transporters, and permeases in infants fed by secretor CMs contributed to the promotion of these bacteria in infants. Our data highlight the important role of fucosylated milk glycans in shaping the gut microbiome of infants and provide a solid foundation for development of "personalized" nutrition for Chinese infants. IMPORTANCE Human milk glycans provide a broad range of carbon sources for gut microbes in infants. Levels of protein glycosylation in human milk vary during lactation and may also be affected by the stages of gestation and lactation and by the secretor status of the mother. This was the first study to evaluate systematically dynamic changes in human milk oligosaccharides and fucosylated N-glycans in the milk of Chinese mothers with different secretor statuses during 6 months of lactation. Given the unique single nucleotide polymorphism site (rs1047781, A385T) on the fucosyltransferase 2 gene among Chinese populations, our report provides a specific insight into the milk glycobiome of Chinese mothers, which may exert effects on the gut microbiota of infants that differ from findings from other study cohorts.},
}

@article {pmid30637337,
year = {2018},
author = {Bayer, K and Jahn, MT and Slaby, BM and Moitinho-Silva, L and Hentschel, U},
title = {Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00150-18},
pmid = {30637337},
issn = {2379-5077},
abstract = {Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for "Candidatus Poribacteria" and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.},
}

@article {pmid30636240,
year = {2018},
author = {Kamińska, E},
title = {[The role of emollients in atopic dermatitis in children].},
journal = {Developmental period medicine},
volume = {22},
number = {4},
pages = {396-403},
pmid = {30636240},
issn = {1428-345X},
abstract = {Atopic dermatitis is a chronic inflammatory disease characterized by recurrent flares, intense itching, erythema, dry skin resulting from skin barrier defects, and staphylococcal infections. Multiple factors may affect the skin`s normal barrier function, including filaggrin gene mutations, immune dysregulation, altered skin microbiome, altered lipids in stratum corneum, or deficiency of antimicrobial peptides AMPs. The disease mainly affects children, causing a considerable impact on the quality of their life; its first manifestations occur with up to 90% of cases before the age of 5. For years emollients have been known as oily substances used to treat rough, scaling, xerotic conditions to make skin flexible and soft. Recently, we have learned that emollients can also moisten and hydrate dry skin, so the terms "emollient" and "moisturizer" are often used interchangeably. According to current management guidelines on atopic dermatitis prepared by dermatological societies, long-term emollient application direct to the skin and as bath additives are the basic therapy of atopic dermatitis. Emollients may be used in monotherapy or - in the flares - in conjunction with topical corticosteroids or calcineurin inhibitors. Clinical trials proved that regular emollient application moistens and hydrates the skin and helps the skin maintain a defensive barrier effect as well as reduces the amount of topical corticosteroids needed for atopic eczema in infants, children and adult patients. The results of trials and long clinical experience proved that emollients are safe and effective in patients with atopic dermatitis. This paper presents information based on recent knowledge concerning emollients: an overview of emollient components, their properties, mechanism of action, and the role they play in atopic eczema, as well as the results of clinical trials performed in children with atopic dermatitis.},
}

@article {pmid30636005,
year = {2019},
author = {Untersmayr, E and Bax, HJ and Bergmann, C and Bianchini, R and Cozen, W and Gould, HJ and Hartmann, K and Josephs, DH and Levi-Schaffer, F and Penichet, ML and O'Mahony, L and Poli, A and Redegeld, F and Roth-Walter, F and Turner, MC and Vangelista, L and Karagiannis, SN and Jensen-Jarolim, E},
title = {AllergoOncology: microbiota in allergy and cancer - an EAACI position paper.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.13718},
pmid = {30636005},
issn = {1398-9995},
abstract = {The microbiota can play important roles in the development of human immunity and the establishment of immune homeostasis. Lifestyle factors including diet, hygiene, and exposure to viruses or bacteria, and medical interventions with antibiotics or anti-ulcer medications, regulate phylogenetic variability and the quality of cross-talk between innate and adaptive immune cells via mucosal and skin epithelia. More recently, microbiota and their composition have been linked to protective effects for health. Imbalance, however, has been linked to immune-related diseases such as allergy and cancer, characterized by impaired, or exaggerated immune tolerance, respectively. In this AllergoOncology position paper, we focus on the increasing evidence defining the microbiota composition as a key determinant of immunity and immune tolerance, linked to the risk for development of allergic and malignant diseases. We discuss novel insights into the role of microbiota in disease and patient responses to treatments in cancer and in allergy. These may highlight opportunities to improve patient outcomes with medical interventions supported through a restored microbiome. This article is protected by copyright. All rights reserved.},
}