Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era

OBJECTIVES

Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.

MATERIALS AND METHODS

Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.

RESULTS

Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.

DISCUSSION

We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.

A case of Riley Ruvalcaba syndrome with a novel PTEN mutation accompanied by diffuse testicular microlithiasis and precocious puberty

BACKGROUND

Bannayan Riley Ruvalcaba syndrome (BRRS) is exceedingly rare, with only about 50 reported cases to date.

CASE PRESENTATION

We report a patient with hypoglycemia, precocious puberty and diffuse testicular microlithiasis accompanying BRRS, and think that this case is important in the light of a newly identified mutation in the PTEN gene.

CONCLUSIONS

Close attention must be paid in terms of PTEN mutations in cases of macrocephaly and accompanying neurological and dermatological findings.

Bull's-eye pattern of pancreatic-duct stones on multidetector computed tomography and gene-mutation-associated pancreatitis (GMAP)

PURPOSE

This study prospectively assessed whether the presence of a bull's-eye pattern of pancreatic-duct stones on multidetector computed tomography (MDCT) correlated with gene-mutation-associated pancreatitis (GMAP) and whether other signs suggestive of GMAP can be detected with MDCT.

MATERIALS AND METHODS

Forty-seven patients with chronic calcific pancreatitis underwent genetic testing for CFTR, SPINK1 and PRSS1 mutations and an MDCT scan of the abdomen. Qualitative analysis assessed the presence or absence of pancreatic-duct stones with bull's-eye appearance. Quantitative analysis included the number and maximum diameter of stones and the diameter of the main pancreatic duct.

RESULTS

Fifteen of 47 patients (32%) were positive for gene mutations (GMAP patients). The bull's-eye pattern was found in 10/15 patients (67%) with GMAP and in 4/32 (12%) patients with chronic pancreatitis not associated with GMAP (NGMAP; p<0.0001). The mean diameter of duct stones was 15 mm in patients with GMAP and 10 mm in patients with NGMAP (p<0.04).

CONCLUSIONS

The presence of duct stones with a bull's-eye pattern correlates with GMAP. Duct stones with diameter ≥15 mm are another sign suggestive of GMAP.

[Three cases of pulmonary alveolar microlithiasis in a family and clinical analysis]

OBJECTIVE

To describe the characteristics of 3 cases of pulmonary alveolar microlithiasis in a family, and therefore to improve the understanding of the disease.

METHODS

To analyze the clinical, laboratory and radiological data of three patients with pulmonary alveolar microlithiasis in a family and the relevant literatures were reviewed.

RESULTS

There was a typical manifestation in these three cases of pulmonary alveolar microlithiasis: progressive dyspnoea, cough, family history. Chest X-ray and computed tomography demonstrate: the pulmones was full of high density reflection of intra-alveolar microliths especially in middle-lower lobe and posterior lobe. The etiology of these three cases is still unknown, consanguineous marriage of parents is possible reason. There was not effective therapies to them.

CONCLUSION

Pulmonary alveolar microlithiasis is a disease without clear known etiology and effective therapy. For a patient with radiological features of high density intra-alveolar microliths and a positive family history, the diagnosis should be highly suspected.

Familial pulmonary alveolar microlithiasis diagnosed by bronchoalveolar lavage. A case report

BACKGROUND

Familial alveolar microlithiasis is a rare lung disease. In this study we describe the cytologic features of this disease in bronchoalveolar lavage.

CASE

A 10-year-old girl and her uncle, a 50-year-old man, had dyspnea and diffuse interstitial pattern on chest radiograph with no defined cause at a period of 10 years apart. Open lung biopsy in the girl and transbronchial lung biopsy plus bronchoalveolar lavage (BAL) in the man were per-formed to determine the diagnosis. In cyopen lung biopsy the diagnosis was alveolar microlithiasis. BAL revealed rehtypical microliths (calcospherites), and th transbronchial lung biopsy performed in the same patient failed to disclose superficially reset any significant pathology. In cytologic a smears, extracellular and intracellular concentrically layered purple-brown, round-to-oval microliths were clearly seen. Cyanophilic periodic acid-Schiff positive intracytoplasmic amorphous material was also frequently seen in alveolar macrophages.

CONCLUSION

Familial alveolar microlithiasis is a rare interstitial lung disease that can be easily diagnosed by BAL. This procedure is a very useful tool in diagnosing and classifying some interstitial lung diseases.

TFF peptides and mucins are major components of dacryoliths

PURPOSE

The study was performed to determine whether trefoil factor peptides (TFF) and/or mucins are components of dacryoliths and to gain further insight into dacryolith composition and formation.

METHODS

Twenty dacryoliths found in lacrimal surgery in patients suffering from primary acquired nasolacrimal duct obstruction were analyzed for the presence of TFF peptides (TFF1, 2, 3), mucins (MUC1, 2, 3, 4, 5AC, 5B, 6, 7, 8), defense cells (T- and B lymphocytes, macrophages, neutrophils), and antimicrobial substances (alpha defensins 1-3, secretory phospholipase A(2)) by means of light microscopy, histochemistry, immunohistochemistry, reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR.

RESULTS

All dacryoliths except one revealed clear immunoreactivity for all three TFF peptides. The immunohistochemical distribution of mucins was inhomogeneous throughout the different dacryoliths. However, in some dacryoliths all mucins investigated were detected. MUC8 showed reactivity in 14 out of 15 dacryoliths analyzed by immunohistochemistry. Most dacryoliths contained alpha defensins 1-3 as the secretory product of neutrophils. T and B lymphocytes, macrophages and secretory phospholipase A(2) were only present in single dacryoliths. Quantification of TFF peptide expression supported the immunohistochemical finding that all three TFF peptides are augmented in dacryoliths.

CONCLUSIONS

Dacryoliths consist partly of secreted mucins comparable with the mucin spectrum of the epithelium of healthy nasolacrimal ducts. Beside TFF1 and TFF3, both of which are produced under healthy circumstances, TFF2 is additionally induced and secreted in cases of dacryolithiasis. All three TFF peptides appear to be augmented in dacryoliths. With regard to their rheologic properties, TFF peptides may play a functional role in dacryolith formation. However, our results raise the question of whether TFF peptides per se influence dacryolith formation or whether their secretion, as in secretion of mucins and alpha defensins 1-3, is merely a secondary phenomenon.

[Multiple enterolithiasis, coexisting with bladder and gallbladder lithiasis, associated with colon adenocarcinoma]

Enteroliths are calculi primarily formed in the intestine. Enterolithiasis is a rare condition frequently associated with intestinal stasis. Usually it causes no symptoms in most cases, but it can be an important diagnostic clue in patients presenting intestinal occlusive symptoms. We report a case of multiple enterolithiasis, very infrequent pathology, coexisting with bladder and gall bladder lithiasis in a patient with colon adenocarcinoma. Diagnosis was made by X-rays and CT images. Calculi were analysed by several methods: chemical, infrared spectroscopy, stereoscopic microscopy and atomic emission spectroscopy; they showed that caluli are made up of organic material and whilokita (calcium and magnesium ortophosphate). No risk factors for lithogenesis were found in this patient excluding the intestinal stasis caused by intestinal narrowing as a result of adenocarcinoma. Genetic factors are suggested as main contributors to hyperlithogenesis observed in this patient. The physiopathological conditions were studied in depth and literature about this subject reviewed.

Profiling of gene expression associated with hepatolithiasis by complementary DNA expression array

By use of cDNA expression array method, we compared the expression profiles of genes in hepatolithiasis tissues with those of paired normal tissues. Expression of 1176 cancer related genes that include 33 tumor suppressor genes, 100 proto-oncogenes and 37 DNA damage repair genes were examined in this study. We found that expression of tumor suppressor genes and proto-oncogenes was systemically activated in hepatholithiasis tissues, suggesting that expression of genes controlling cell growth becomes unstable in liver lobe of hepatolithiasis. In contrast, expression of DNA damage repair genes were not activated but rather remained unchanged in hepatholithiasis tissues, suggesting that repair process is not strongly activated but rather impaired in hepatholithiasis tissues.

Pulmonary alveolar microlithiasis: clinical features, evolution of the phenotype, and review of the literature

Pulmonary alveolar microlithiasis (PAM) (MIM 265100) is a rare, autosomal recessive pneumopathy characterized by intra-alveolar formation and accumulation of tiny, roundish corpuscles called "microliths". The name "alveolar microlithiasis" was first used by Puhr in 1933; since then, several reports have appeared, and over 300 individuals with this condition have been reported. We have reviewed the PAM cases in the literature in light of personal experience, focusing on medical implications, disease diagnosis and progression over time, familial predisposition, and geographical and sex distribution. This study confirms autosomal recessive inheritance and does not support the role of other, non-genetic, factors in the pathogenesis of PAM.

Genetic susceptibility to fibrocalculous pancreatic diabetes in Bangladeshi subjects: a family study

Fibrocalculous pancreatic diabetes (FCPD) is an uncommon cause of diabetes, seen mainly in developing countries. A family-based study was carried out in 67 Bangladeshi families, consisting of a proband with FCPD and both parents, to determine whether an association exists between FCPD susceptibility and either the major histocompatiblity complex (MHC) or insulin gene (INS) loci. HLA-DQB1 typing was done using allele-specific primers, and INS was typed using the restriction enzyme HphI. Three microsatellites (TNFa, TNFc and TNFd), from within and flanking the TNF-LT locus, were used for MHC Class IV typing and a PCR-RFLP assay was used to define the -308G/A TNF promoter polymorphism. The extended transmission disequilibrium test (ETDT) was used for statistical analysis. An overall association was observed between FCPD and HLA-DQB1 (P = 0.003), that was largely due to a positive association with HLA-DQB1*0302 and a negative association with HLA-DQB1*0202. Although no association was found between FCPD and TNF-LT microsatellite markers a trend was observed for TNFc (P = 0.037, Pc = 0.15). No association was found between FCPD and INS (P = 0.26). This study confirms an association between FCPD and the MHC using a family-based study design and the stringent ETDT analysis; a novel protective association was found with HLA-DQB1*0202 in Bangladeshi FCPD subjects. The genetic susceptibility to FCPD has features both similar and dissimilar to T1DM.

Pulmonary alveolar microlithiasis: a rare familial inheritance with report of six cases in a family. Contribution of six new cases to the number of case reports in Turkey

Pulmonary alveolar microlithiasis (PAM) is a lung disease characterized by deposits of calcium within the alveoli. Our aim was to emphasize the familial character and the clinical features of the disease, and to draw attention to the increasing number of Turkish patients reported in the world. We detected 6 cases of PAM. Three cases had been diagnosed 4 years earlier, and 3 new cases were detected during the screening of the family members. All patients were male and the mean age was 11.5 ranging between 5 and 29 years. Five of the patients were cousins and the other one was their uncle. Radiographic studies showed a sand-like appearance in all patients. One case showed small subpleural bullae and bronchiectatic changes in both lower lobes in recent high-resolution CT scans, while his CT performed 4 years ago showed only sand-like appearance. The cases were diagnosed with the demonstration of microliths by bronchoalveolar lavage in 5 patients and transbronchial biopsy in 1. Recently reported cases from Turkey have constituted a considerable percentage among all cases in the world. In conclusion, (1) our patients constitute one of the largest series of cases reported in one family in the world. The disease seems to have familial and racial characteristics. The Turkish race has to be further investigated for genetic transmission. (2) Contrary to female predominance in previous reports, all 6 cases were male and 5 of them were below 12 years of age. (3) The disorder may show rapid progression in some cases probably due to the severity of the genetic disturbance.

Radiolucent pancreatic lithiasis: a precursor stage for calcified pancreatic lithiasis or a new entity?

OBJECTIVE

Radiolucent pancreatic lithiasis (RPL) has been identified as a different entity from calcified pancreatic lithiasis. The purpose of this study is to evaluate the frequency, characteristics and evolution of RPL.

PATIENTS

Between 1983 and 1995, 278 consecutive patients who presented with pancreatic lithiasis were studied. Forty-four patients had RPL (15.8%): 27 had pure radiolucent stones (PRS) (group 1), 5 had pure radiolucent stones combined with evenly calcified stones (ECS) (group 2), 2 had target calculi (TC) (radiolucent core with calcified shell) (group 3), 10 had TC combined with ECS (group 4).

RESULTS

Among the 27 patients with PRS, there were 19 males with a mean age of 41 years. PRS were mainly located in the head of the pancreas with a mean diameter of 5 mm (range 3-26 mm). Seven patients among 27 with PRS (26%) were less than 20 years old (juvenile form) or more than 60 years old (senile form). They were characterized by no or low alcohol consumption and a high rate of attacks of acute pancreatitis. In group 1, PRS turned to more advanced calcified stages in 6/16 of patients (37%) followed in 30 to 144 months with a prior stage of TC in 2 cases. An evolution toward more calcified stages (TC or ECS) occurred in half of the patients belonging to group 2 and 4 in 36 to 84 months. Genetic disposition and alcohol consumption could account for the evolution toward more calcified stages. A genetic factor is suggested by a rapid evolution to evenly calcified stones in two aged children 8 and 10 years and by a high frequency of familial cases in patients belonging to groups 2 and 4 (60% and 20%) as compared to group 1 with PRS (4%). Alcohol consumption could accelerate the calcifying process since patients belonging to groups 2 and 4 had a significantly higher alcohol consumption than those with PRS (group 1).

CONCLUSION

RPL is a heterogeneous pancreatic disease including juvenile and senile presentation which may represent about 15% of pancreatic lithiasis. Evolution towards calcified stages (PRS then TC then ECS) occurred in 37-50% of cases and could be related to a genetic factor and increased alcohol consumption.

Pulmonary alveolar microlithiasis associated with calcifications in the seminal vesicles

Pulmonary alveolar microlithiasis is an inherited disorder of unknown etiology. It is a rare disease characterized by calcified intraalveolar microgranules. Several hypotheses on the etiopathogenesis have been put forward, such as increased intestinal calcium resorption and retention. This case report of pulmonary alveolar microlithiasis is associated with punctate calcifications in the seminal vesicles.

Pulmonary alveolar microlithiasis in children

Two asymptomatic Turkish sibs are presented, a 4-year-old boy and his 7-year-old sister, with pulmonary alveolar microlithiasis (PAM) confirmed by transbronchial lung biopsy and bronchoalveolar lavage. Chest radiographs and high resolution CT demonstrated widespread intra-alveolar calcifications in both lungs. The lesions were sharply defined and less than 1 mm in diameter. CT documented a high concentration of microliths along the bronchovascular bundles, the intralobular fissure and the (sub)pleural lung parenchyma. The combination of bronchoalveolar lavage and roentgenographic appearance in high resolution CT are characteristic and pathognomonic, and can confirm the diagnosis. The more severe changes in the elder sib and the radiographic controls suggest that the pulmonary disease may be progressive in our patients. The described family of consanguineous, unaffected parents with two affected and one healthy child confirmed the autosomal recessive inheritance of PAM (McKusick 265100). In addition, the affected girl had autosomal recessive Waardenburg-anophthalmia syndrome (McKusick 206920), raising the question of whether this is a chance occurrence or possibly a contiguous gene syndrome.

[Pulmonary alveolar microlithiasis in two siblings]

The study of two brothers with pulmonary alveolar microlithiasis (MLA) a rare lung alteration with autosomic recessive character is presented. In one case the lung biopsy made the diagnosis by the identification of multiple calcospherites. The importance of the familiar study is stressed, as a sister with the same radiographic image was discovered this way. The literature is revised and the main data of MLA are presented; the radiologic images and histopathologic findings are commented.

[Hereditary protein lithiasis and calcium lithiasis: two different forms of hereditary pancreatitis]

We previously reported that the most frequent cases of chronic pancreatitis were the consequence of pancreatic lithiasis and that there were different forms of pancreatic lithiasis with different etiologies and composition of calculi. The most frequent form is the calcic lithiasis, generally due to nutritional disorders. The second most frequent form is proteic lithiasis. In this paper, we report 1.) Ten hereditary cases on a total of 36 patients presenting with proteic lithiasis (age at clinical onset 15 +/- 12 years); 2.) one hereditary case on a total of 150 patients with proteic lithiasis. In these two different maladies, the transmission seems to be dominant, autosomal with incomplete penetrance. Hereditary pancreatitis is therefore a group of at least two different diseases, hereditary protein lithiasis, the most frequent one and hereditary calcic lithiasis exceptional.

Pulmonary alveolar microlithiasis in a Saudi child and two cousins

Pulmonary alveolar microlithiasis is a rare disease and only 32 cases have been reported in children under 12 years of age. The first report on Saudi children with this disorder and on affected cousins is presented, supporting the possible hypothesis of it being an autosomal recessive disorder. The importance of differentiating it from other conditions, particularly pulmonary tuberculosis, and the current approach to diagnosis and management are discussed.

Improvement in gas exchange with nasal continuous positive airway pressure in pulmonary alveolar microlithiasis

A 37-yr-old man with pulmonary alveolar microlithiasis (PAM) presented with respiratory failure and cor pulmonale. The FEV1/FVC was 1.4/1.8 L with total lung capacity of 3.2 L using the helium dilution method (54% predicted) and 6.1 L using body plethysmography (102% predicted), indicating large noncommunicating regions. The KCO (transfer factor per liter lung volume) was 3.05 ml/min/mm Hg/L (47% predicted). Despite home oxygen (3 L/min) and diuretic therapy, the patient remained hypoxic (PaO2, 55 mm Hg) and incapacitated with dyspnea. Nasal continuous positive airway pressure (nCPAP) at 12 cm H2O and oxygen at 1 L/min improved his oxygenation (PaO2, 93 mm Hg), and introduction of this regimen at night resulted in subjective improvement in daytime function. A Grandjean right heart catheter was introduced at the bedside, and the multiple inert gas elimination technique (MIGET) was used to measure ventilation and blood flow distributions at ambient pressure and with the addition of 10 cm H2O nCPAP. The patient had severe pulmonary hypertension (mean Ppa, 57 mm Hg) and severe hypoxemia (PaO2 37 mm Hg), which was mainly due to shunt (16% of cardiac output) and a broadening of the main mode of the ventilation-perfusion (VA/Q) distribution (log SD Q, 0.94). There was a significant reduction in shunt during nCPAP to 6% of cardiac output without increasing Ppa, and this effect appeared to extend past the period of application. We conclude that nCPAP reduces intrapulmonary shunt in this rare condition and allows for correction of hypoxemia with a smaller oxygen flow rate.

Radiolucent and calcified pancreatic lithiasis: two different diseases. Role of alcohol and heredity

One hundred and eighteen consecutive patients presenting with pancreatic calculi have been studied by means of plain films of the abdomen and endoscopic retrograde cholangiopancreatography. Patients were divided into the following groups: 1) Evenly calcified calculi, 74 patients, 66 men, aged at onset (M +/- SM) 40 +/- 10 years; daily consumption of alcohol, 157 +/- 121 g, and of tobacco, 26 +/- 15 cigarettes. Two patients presented with another case in the same family. Composition of calculi--at least 95% calcium salts and a degraded form of lithostathine S (formerly called PSP S2-5)--was similar in the Occidental alcoholic and in the tropical form: calcified calculi are probably related to alcohol and nutritional disorders. 2) Radiolucent stones, 17 patients, 12 men and 5 women, aged at onset 38 +/- 18 years. These patients had a low alcohol and tobacco consumption. There were four familial cases. 3) Radiolucent core with a calcified shell (target calculi), 27 cases, 23 men; age at onset, 38 +/- 15 years; daily ethanol consumption, 111 +/- 93, and tobacco, 19 +/- 15 cigarettes. There were two familial cases. It has been shown that these calculi originated from transparent calculi that later calcified. The frequency of women and of familial cases was significantly greater in groups 2 + 3 than in group 1. The consumption of alcohol and tobacco and the proportion of men were significantly lower in group 2 than in groups 1 and 3. We discuss the role of heredity in lithostathine precipitation and of alcohol in calcium precipitation.(ABSTRACT TRUNCATED AT 250 WORDS)

[Pulmonary alveolar microlithiasis. A familial presentation in two sisters]

Alveolar lung microlithiasis is a rare disease of unknown etiology, with familial feature in 50% of the cases. The onset of this disease in 2 sisters is presented.

[Quantification of pulmonary alveolar microlithiasis in the CT]

Pulmonary alveolar microlithiasis is a rare, familial disease with massive symmetrical intra-alveolar calcium deposition. Conventional CT findings and CT measurements with a dual energy technique were carried out in a 26-year-old patient suffering from this disease. The importance of the findings in the differential diagnosis and for estimating the progression and prognosis of the disease is discussed.

[Pulmonary alveolar microlithiasis in 2 Moroccan sisters]

The histories of two Moroccan sisters with pulmonary alveolar microlithiasis are described. Two years follow-up is available. The elder girl has no complaints, her two years younger sister becomes dyspnoeic on exercise. Pulmonary alveolar microlithiasis is a rare condition, which occurs mostly as a familiary disease. On pathologic examination characteristic calcifications are found in the alveoli. The radiographic picture of the chest is quite typical. A short review of the literature is presented.

Pulmonary alveolar microlithiasis

Three cases of pulmonary alveolar microlithiasis are reported at the symptom-free stage of this condition. Two were siblings.