Elevated rates of horizontal gene transfer in the industrialized human microbiome.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Dizziness: Evaluation and Management.

Dizziness is a common but often diagnostically difficult condition. Clinicians should focus on the timing of the events and triggers of dizziness to develop a differential diagnosis because it is difficult for patients to provide quality reports of their symptoms. The differential diagnosis is broad and includes peripheral and central causes. Peripheral etiologies can cause significant morbidity but are generally less concerning, whereas central etiologies are more urgent. The physical examination may include orthostatic blood pressure measurement, a full cardiac and neurologic examination, assessment for nystagmus, the Dix-Hallpike maneuver (for patients with triggered dizziness), and the HINTS (head-impulse, nystagmus, test of skew) examination when indicated. Laboratory testing and imaging are usually not required but can be helpful. The treatment for dizziness is dependent on the etiology of the symptoms. Canalith repositioning procedures (e.g., Epley maneuver) are the most helpful in treating benign paroxysmal positional vertigo. Vestibular rehabilitation is helpful in treating many peripheral and central etiologies. Other etiologies of dizziness require specific treatment to address the cause. Pharmacologic intervention is limited because it often affects the ability of the central nervous system to compensate for dizziness.

Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles).

Triparma laevis f. inornata is a unicellular alga belonging to the Bolidophyceae, which is most closely related to diatoms. Like diatoms, T. laevis f. inornata has a siliceous cell wall. The cell wall of T. laevis f. inornata consists of four round plates (three shields and one ventral plate) and one dorsal and three girdle plates. But, unlike diatoms, T. laevis f. inornata cells can grow when concentrations of silica are depleted. We took advantage of this ability, using TEM to study the ontogeny of the siliceous plate, pattern center formation, and development. Two types of pattern centers (annulus and sternum) were observed in the early and middle stage of plate formation. During their formation, the annuli were initially crescent-shaped but eventually their ends fused to make a ring. Only outward silica deposition of the branching ribs occurred on the growing annulus until it became a ring, resulting in an unfilled circle inside the annulus. The pattern center of the shield plate was always an annulus, but in ventral plates both annulus and sternum were observed. The annuli and sterna in T. laevis f. inornata round plates were very similar to the annuli and sterna in diatom valves. These results suggested that the round plates of Parmales are homologous to diatom valves. This information on the plate ontogeny of T. laevis f. inornata provides new insights into the evolution of the siliceous cell wall in the Parmales and diatoms.

Long Term Survivals in Aggressive Primary Brain Malignancies Treated With an Adjuvant Ketogenic Diet.

Aggressive primary brain tumors (APBT) glioblastoma multiforme and grade IV astrocytoma are treated with multimodality treatments that include surgery to remove as much tumor as possible without sacrificing neurological function followed by radiation therapy and chemotherapy usually temozolomide. Survivals in adults are in the range of 8-16 months. The addition of a ketogenic diet (KD) to rodents with transplanted brain tumors increased survival in nine of 11 animals to over 299 days compared to survival in untreated controls of 33 days and radiation only controls of 38 days. We treated humans with APBT with standard of care neurosurgery immediately followed by 6 weeks of an adjuvant ketogenic diet concurrent with radiation therapy and temozolomide. Twice daily measurements of blood ketones and glucose were recorded and the patients' diet was modified toward the goal of maintaining blood ketone levels approaching 3 mM. Of the nine patients who completed the protocol three younger patients age 32, 28, and 22 at enrollment are alive and employed with clinically stable disease and brain images 74, 58, and 52 months since diagnosis. All the six older patients mean age 55 have died with disease progression detected on average 8 months after Dx. In conclusion: 1. It is possible to implement and maintain dietary induced ketosis in patients with APBT; 2. The longer survivals observed in younger patients treated with KD need to be confirmed in larger studies that should be focused on younger patients possibly under age 40.

Cabbage and Sauerkraut Consumption in Adolescence and Adulthood and Breast Cancer Risk among US-Resident Polish Migrant Women.

BACKGROUND: Breast cancer (BC) incidence and mortality are lower in Poland than in the United States (US). However, Polish-born migrant women to US approach the higher BC mortality rates of US women. We evaluated the association between consumption of cabbage/sauerkraut foods and BC risk in Polish-born migrants to US. METHODS: We conducted a case-control study of BC among Polish-born migrants in Cook County and the Detroit Metropolitan Area. Cases (n = 131) were 20-79 years old with histological/cytological confirmation of invasive BC. Population-based controls (n = 284) were frequency matched to cases on age and residence. Food frequency questionnaires assessed diet during adulthood and age 12-13 years. Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated with conditional logistic regression. Consumption of total, raw/short-cooked, and long-cooked cabbage/sauerkraut foods was categorized as low, medium, or high (frequency of servings/week). RESULTS: Higher consumption of total and raw/short-cooked cabbage/sauerkraut foods, during both adolescence and adulthood, was associated with a significantly lower BC risk. Consumption of long-cooked cabbage/sauerkraut foods was low and not significantly associated with risk. The multivariate OR for total cabbage/sauerkraut consumption, high vs. low (>4 vs. ≤2 servings/week) during adolescence was 0.36 (95% CI = 0.18-0.71, ptrend < 0.01) and 0.50 (95% CI = 0.23-1.06, ptrend = 0.08) during adulthood. For raw/short-cooked cabbage/sauerkraut (>3 vs. ≤1.5 servings/week), the ORs were 0.35 (95% CI = 0.16-0.72, ptrend < 0.01) during adolescence and 0.37 (95% CI = 0.17-0.78, ptrend < 0.01) during adulthood. For joint adolescent/adult consumption of raw/short-cooked cabbage/sauerkraut foods, (high, high) vs. (low, low), the OR was 0.23 (95% CI = 0.07-0.65). The significant association for high adolescent consumption of raw/short-cooked cabbage/sauerkraut foods and reduced BC risk was consistent across all levels of consumption in adulthood. CONCLUSION: Greater consumption of total and raw/short-cooked cabbage/sauerkraut foods either during adolescence or adulthood was associated with significantly reduced BC risk among Polish migrant women. These findings contribute to the growing literature suggesting a protective effect of a potentially modifiable factor, cruciferous vegetable intake, on breast cancer risk.

A repurposed tool: the Programme Evaluation SOAP Note.

CONTEXT: Doctors have used the subjective-objective-assessment-plan (SOAP) note format to organise data about patient problems and create plans to address each of them. We retooled this into the 'Programme Evaluation SOAP Note', which serves to broaden the clinician faculty member's perspective on programme evaluation to include the curriculum and the system, as well as students. METHODS: The SOAP Note was chosen as the method for data recording because of its familiarity to clinician-educators and its strengths as a representation of a clinical problem-solving process with elements analogous to educational programme evaluation. We pilot-tested the Programme Evaluation SOAP Note to organise faculty members' interpretations of integrated student performances during the Year 3 patient care skills objective structured clinical examination (OSCE). RESULTS: Eight community clerkship directors and lead clerkship faculty members participated as observers in the 2007 gateway examination and completed the Programme Evaluation SOAP Note. Problems with the curriculum and system far outnumbered problems identified with students. CONCLUSIONS: Using the Programme Evaluation SOAP Note, clerkship leaders developed expanded lists of 'differential diagnoses' that could explain possible learner performance inadequacies in terms of system, curriculum and learner problems. This has informed programme improvement efforts currently underway. We plan to continue using the Programme Evaluation SOAP Note for ongoing programme improvement.

Author Correction: Chloropicophyceae, a new class of picophytoplanktonic prasinophytes.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum.

The dinoflagellate Lepidodinium chlorophorum possesses "green" plastids containing chlorophylls a and b (Chl a+b), unlike most dinoflagellate plastids with Chl a+c plus a carotenoid peridinin (peridinin-containing plastids). In the present study we determined 8 plastid-encoded genes from Lepidodinium to investigate the origin of the Chl a+b-containing dinoflagellate plastids. The plastid-encoded gene phylogeny clearly showed that Lepidodinium plastids were derived from a member of Chlorophyta, consistent with pigment composition. We also isolated three different glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes from Lepidodinium-one encoding the putative cytosolic "GapC" enzyme and the remaining two showing affinities to the "plastid-targeted GapC" genes. In a GAPDH phylogeny, one of the plastid-targeted GapC-like sequences robustly grouped with those of dinoflagellates bearing peridinin-containing plastids, while the other was nested in a clade of the homologues of haptophytes and dinoflagellate genera Karenia and Karlodinium bearing "haptophyte-derived" plastids. Since neither host nor plastid phylogeny suggested an evolutionary connection between Lepidodinium and Karenia/Karlodinium, a lateral transfer of a plastid-targeted GapC gene most likely took place from a haptophyte or a dinoflagellate with haptophyte-derived plastids to Lepidodinium. The plastid-targeted GapC data can be considered as an evidence for the single origin of plastids in haptophytes, cryptophytes, stramenopiles, and alveolates. However, in the light of Lepidodinium GAPDH data, we need to closely examine whether the monophyly of the plastids in the above lineages inferred from plastid-targeted GapC genes truly reflects that of the host lineages.

Investigating the Ketogenic Diet As Treatment for Primary Aggressive Brain Cancer: Challenges and Lessons Learned.

Survival of glioblastoma multiforme (GBM) with the current recommended treatment is poor. Reported median survivals are approximately 8-15 months. Based on recent publications from animal models, combining cancer drugs, radiation, and diet-metabolic treatments may be a new route to better survivals. To investigate this possibility, we have begun a clinical trial that has enrolled 15 subjects using a ketogenic diet (KD) as an addition to current standard treatments that include surgery, radiation therapy, and chemotherapy. Of the 15 enrolled, 10 completed the protocol. This perspective describes the challenges and lessons learned during this clinical trial and discusses the critical elements that are essential for investigating treatment with a KD. We also reviewed and compared various types of KDs. We believe that the diet selected should be standardized within individual clinical trials, and more importantly, the patients' blood should be monitored for glucose and ketones twice daily so that the supervising dietitian can work with the patient and their caregivers to make appropriate changes in the diet. Compliance with the diet is best in highly motivated patients who have excellent home support from a family member or a friend who can help to overcome administrative, physical, and cognition deficiencies associated with the disease. Treatment of GBM using a KD represents a reasonable investigative approach. This perspective summarizes the challenges and lessons learned implementing and continuing KD therapy while the patients are concurrently being treated with radiation and chemotherapy.

PURL: First-time, mild diverticulitis: Antibiotics or watchful waiting?

Don't jump to antibiotic Tx for mild, uncomplicated diverticulitis, a recent RCT says. Observation may be just as effective.

Issues in Nutrition: Dietary Considerations in Select Chronic Conditions.

Chronic diseases that affect the gastrointestinal tract also tend to affect nutrition. The incidence of chronic liver disease is increasing. As the prevalence of obesity rises, so do the incidences of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis. Patients with chronic liver disease usually have some degree of malnutrition. In the absence of encephalopathy, patients with chronic liver disease should consume more protein than that in the average diet. There is some controversy about whether diet plays a role in the development of inflammatory bowel disease. Patients with ulcerative colitis and Crohn disease frequently present with weight loss as a symptom, and require careful nutritional assessment. Exclusive enteral nutrition plays an important role in inducing remission in children with Crohn disease but the same is not true in adults. Celiac disease is a relatively common enteropathy characterized by an autoimmune response in the intestinal lining. Patients with celiac disease should avoid eating gluten, which is found in wheat, soy, and barley. There is no evidence that gluten avoidance results in improved health outcomes in patients who are not gluten intolerant.

Issues in Nutrition: Nutritional Assessment of Adults.

The assessment of nutritional status in adults should begin with a complete history, including intake of fruits and vegetables, sources of fat, and added sugar (eg, sugar-sweetened beverages). The history should include social factors that may impede a patient's ability to obtain food, as well as any factors that might interfere with preparing, chewing, and digesting food and absorbing nutrients. The physical examination should include measurement of height and weight and calculation of body mass index. It also may include measurements of waist circumference and waist to hip ratio, and an evaluation of strength. Laboratory evaluation should include measurement of albumin, prealbumin, and other markers of total body protein stores. No biomarker is completely sensitive or specific. With a range of dietary patterns, it is possible for nutritional gaps specific to those patterns to develop. Identification of a single nutrient deficiency typically reflects an overall weakness in the diet. The Mediterranean and Dietary Approaches to Stop Hypertension (DASH) diets have the most evidence to support them as healthy diets.

Issues in Nutrition: Dietary Supplements.

The majority of American adults report use of one or more dietary supplements every day or occasionally. The Dietary Supplement Health and Education Act of 1994 defines dietary supplements and regulates their manufacture and distribution. One of the most commonly used supplements is vitamin D. Measurement of serum levels of vitamin D must be undertaken with the caveats that different laboratories define normal levels differently, and that there is rarely a clinical correlation with the actual level. Patients should understand that supplements should not be used to excess, as there are toxicities and other adverse effects associated with most of them. There currently is considerable research being performed on probiotics and how the gut microbiome affects health and disease states. Protein supplements may be useful in reducing mortality rates in elderly patients but they do not appear to increase quality of life. If used, protein supplements should contain essential amino acids. Casein and whey supplements, derived from dairy sources, help transport essential amino acids to tissues. Although there have been many studies investigating the role of vitamin supplements in disease prevention, there have been few conclusive positive results.

Issues in Nutrition: Carbohydrates.

Carbohydrates include sugars, starches, and dietary fibers. Resistant starches resemble fiber in their behavior in the intestinal tract, and may have positive effects on blood glucose levels and the gut microbiome. Fibers are classified as soluble and insoluble, but most fiber-containing foods contain a mixture of soluble and insoluble fiber. Soluble fiber has been shown to lower low-density lipoprotein cholesterol levels. Many artificial sweeteners and other sugar substitutes are available. Most natural sources of sweeteners also are energy sources. Many artificial sweeteners contain no kilocalories in the amounts typically used. Sugar alcohols may have a laxative effect when consumed in large amounts. Glycemic index and glycemic load are measurements that help quantify serum glucose response after ingestion of particular foods. These measurements may be affected by the combination of foods consumed in a given meal, and the glycemic index may vary among individuals eating the same meal. Eating foods with a low glycemic index may help prevent development of type 2 diabetes. There is no definitive evidence to recommend low-carbohydrate diets over low-fat diets for long-term weight loss; they are equally effective.

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters.

Prasinophytes clade VII is a group of pico/nano-planktonic green algae (division Chlorophyta) for which numerous ribosomal RNA (rRNA) sequences have been retrieved from the marine environment in the last 15 years. A large number of strains have also been isolated but have not yet received a formal taxonomic description. A phylogenetic analysis of available strains using both the nuclear 18S and plastidial 16S rRNA genes demonstrates that this group composes at least 10 different clades: A1-A7 and B1-B3. Analysis of sequences from the variable V9 region of the 18S rRNA gene collected during the Tara Oceans expedition and in the frame of the Ocean Sampling Day consortium reveal that clade VII is the dominant Chlorophyta group in oceanic waters, replacing Mamiellophyceae, which have this role in coastal waters. At some location, prasinophytes clade VII can even be the dominant photosynthetic eukaryote representing up to 80% of photosynthetic metabarcodes overall. B1 and A4 are the overall dominant clades and different clades seem to occupy distinct niches, for example, A6 is dominant in surface Mediterranean Sea waters, whereas A4 extend to high temperate latitudes. Our work demonstrates that prasinophytes clade VII constitute a highly diversified group, which is a key component of phytoplankton in open oceanic waters but has been neglected in the conceptualization of marine microbial diversity and carbon cycle.

Chloropicophyceae, a new class of picophytoplanktonic prasinophytes.

Prasinophytes are a paraphyletic group of nine lineages of green microalgae that are currently classified either at the class or order level or as clades without formal taxonomic description. Prasinophyte clade VII comprises picoplanktonic algae that are important components of marine phytoplankton communities, particularly in moderately oligotrophic waters. Despite first being cultured in the 1960s, this clade has yet to be formally described. Previous phylogenetic analyses using the 18S rRNA gene divided prasinophyte clade VII into three lineages, termed A, B and C, the latter formed by a single species, Picocystis salinarum, that to date has only been found in saline lakes. Strains from lineages A and B cannot be distinguished by light microscopy and have very similar photosynthetic pigment profiles corresponding to the prasino-2A pigment group. We obtained phenotypic and genetic data on a large set of prasinophyte clade VII culture strains that allowed us to clarify the taxonomy of this important marine group. We describe two novel classes, the Picocystophyceae and the Chloropicophyceae, the latter containing two novel genera, Chloropicon and Chloroparvula, and eight new species of marine picoplanktonic green algae.

A haptophyte bearing siliceous scales: ultrastructure and phylogenetic position of Hyalolithus neolepis gen. et sp. nov. (Prymnesiophyceae, Haptophyta).

A haptophyte alga bearing hyaline but conspicuous scales was discovered in surface water samples of Shiribeshi Seamount, Japan. X-ray elemental analysis confirmed that silica was the major element in these scales. These scales were hat-shaped, ellipsoidal in top view, 4-6mum wide and 5-7mum long, perforated by several small pores, and were deposited on cells in several layers. Beneath the siliceous scale layers, organic scales were present, which are typical of haptophytes. The cells were non-motile despite having two short flagella hidden in the scale case. The haptonema, extended over the scale case, and one and a half times the cell length. The intracellular features were typical of haptophytes, including the peripheral endoplasmic reticulum (PER), Golgi cisternae with peculiar dilations, and the flagellar apparatus. The siliceous scales were produced in vesicles in the posterior region of the cell. Motile cells lacking silica scales were observed occasionally when cultures were maintained at lower temperatures and under oligotrophic conditions. This alga was described as Hyalolithus neolepis gen. et sp. nov. Phylogenetic analysis using the SSU rDNA and rbcL gene sequences indicated that Hyalolithus is a member of the Prymnesiales and falls in a clade including Prymnesium, Platychrysis, and Chrysochromulina polylepis. Based on these results, the evolutionary implications of the presence of silicified scales in haptophytes is discussed.

Application of cryopreservation to genetic analyses of a photosynthetic picoeukaryote community.

Cryopreservation is useful for long-term maintenance of living strains in microbial culture collections. We applied this technique to environmental specimens from two monitoring sites at Sendai Bay, Japan and compared the microbial diversity of photosynthetic picoeukaryotes in samples before and after cryopreservation. Flow cytometry (FCM) showed no considerable differences between specimens. We used 2500 cells sorted with FCM for next-generation sequencing of 18S rRNA gene amplicons and after removing low-quality sequences obtained 10,088-37,454 reads. Cluster analysis and comparative correlation analysis of observed high-level operational taxonomic units indicated similarity between specimens before and after cryopreservation. The effects of cryopreservation on cells were assessed with representative culture strains, including fragile cryptophyte cells. We confirmed the usefulness of cryopreservation for genetic studies on environmental specimens, and found that small changes in FCM cytograms after cryopreservation may affect biodiversity estimation.

Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms.

Bolidomonas is a genus of picoplanktonic flagellated algae that is closely related to diatoms. Triparma laevis, a species belonging to the Parmales, which are small cells with a siliceous covering, has been shown to form a monophyletic group with Bolidomonas. We isolated several novel strains of Bolidophyceae that have permitted further exploration of the diversity of this group using nuclear, plastidial and mitochondrial genes. The resulting phylogenetic data led us to formally emend the taxonomy of this group to include the Parmales within the Bolidophyceae, to combine Bolidomonas within Triparma and to define a novel species, Triparma eleuthera sp. nov. The global distribution of Bolidophyceae was then assessed using environmental sequences available in public databases, as well as a large 18S rRNA V9 metabarcode data set from the Tara Oceans expedition. Bolidophyceans appear ubiquitous throughout the sampled oceans but always constitute a minor component of the phytoplankton community, corresponding to at most ~4% of the metabarcodes from photosynthetic groups (excluding dinoflagellates). They are ~10 times more abundant in the small size fraction (0.8-5 µm) than in larger size fractions. T. eleuthera sp. nov. constitutes the most abundant and most widespread operational taxonomic unit (OTU) followed by T. pacifica, T. mediterranea and the T. laevis clade. The T. mediterranea OTU is characteristic of Mediterranean Sea surface waters and the T. laevis clade OTU is most prevalent in colder waters, in particular off Antarctica.