Biosecurity measures designed to reduce the risk of the infectious disease’s introduction in dairy farms by employees and visitors.
\r\n\tIn this book, the different factors of liquefaction, the field methods and laboratory tests to identify a potentially liquefiable soil aim to be reviewed; in addition with history cases (ground behavior during the occurrence of an earthquake, state of stress, deformation, shear strength, flow, etc.).
\r\n\tA very important aspect of this topic is the presentation of the different constructive techniques used to ground improvement (vibrocompaction, dynamic compaction, jet grouting, chemical injection, replacement, etc.), placing special emphasis on those constructive methods used to solve problems on structures already located in areas of low relative density with liquefaction potential, where the installation of monitoring and control equipment is also required (tiltmeters, piezometers, topographic points, seismographs, pressure cells, etc.).
Archaea represent the third domain of life, in addition to Prokaryota, which they more or less physically resemble, and Eukaryota, with which they have more genetic similarities. Many archaea are classified as extremophiles, but those which live in the digestive tract of animals are known as methanogens. Archaeal diversity in the gastrointestinal tract (GIT) is far less than that of bacteria, and more specifically monogastrics have a much lower diversity as compared to herbivorous ruminant animals. In both host types, species belonging to the genus Methanobrevibacter have been cited as the dominant methanogens in the GIT. In fact, Mbr. smithii is the dominant species found in the human GIT, followed by Methanosphaera stadtmanae [1–5]. This lack of relative diversity is largely a function of diet, the presence or absence of other microorganisms, or digestive tract physiology, but it may play a role in human intestinal dysbiosis. A general increase in microbial diversity has been correlated with a healthy gut microbiome that is resistant to physical or biotic disruptions, as there is redundancy in metabolic pathways and the increased competition precludes dominance by one particular taxon. Higher methanogen diversity was correlated with lower breath methane production in humans [1].
\nMethanogens use hydrogen, in the form of free protons, H2 gas, NADH and NADPH cofactors, acetate, or formate, to reduce carbon dioxide and produce methane gas. Thus, methanogens rely on the by-products of bacterial fermentation of carbohydrates (i.e., carbon, hydrogen, acetate, formate, or methanol) as precursor materials required for methanogenesis and their own energy production. Dietary carbohydrates which are not broken down or absorbed by the host are available to bacteria for fermentation [6], and a large amount of unused carbohydrates may consequently increase bacterial fermentation and archaeal methanogenesis. A diet high in fiber and structural carbohydrates, which are largely indigestible to animal and human enzymes (i.e., cellulose, hemicellulose, and lignin), is associated with populations of Methanobrevibacter ruminantium [7], while a diet high in starch and other easily digestible carbohydrates is associated with Mbr. smithii [8, 9]. Mbr. smithii has been shown to improve polysaccharide digestion by GIT bacteria and fungi, and even influence the production of acetate or formate for its own use [10, 11]. Msp. stadtmanae requires methanol, a compound that is the by-product of pectin fermentation, for its methanogenesis pathway, which accounts for its presence in omnivores [1, 2, 5, 12].
\nMethanogens also have a slower growth rate than bacteria, which is sensitive to concentrations of hydrogen required as an electron donor during methanogenesis, as well as other nutrients. Few methanogenic taxa are motile, and these are limited to the order Methanococcales, and the genera Methanospirillum, Methanolobus, Methanogenium, and Methanomicrobium (order: Methanomicrobiales) [13, 14]. This difficulty of remaining situated in the intestines is a limiting factor in methanogen density. In humans, methanogens tend to be denser in the left colon, where fecal matter becomes more solid and transit time slows down [15], but they have also been found in the small intestine [16]. In addition, passing through the gastric stomach is challenging, which may explain why oral and intestinal populations of archaea and bacteria do not share an overlapping diversity [17, 18]. To overcome challenges to intestinal retention, some species of methanogens have adapted to the human colon and are able to thrive. Mbr. smithii produces surface glycans and adhesion-like proteins which improves their interaction with host epithelia and allows for persistence in the gut, as well as wider range of fermentation by-products, which can be used for methanogenesis, allowing for the flexibility of the human diet [3].
\nColonic gases are among the most tangible features of digestion, yet physicians are typically unable to offer long-term relief from clinical complaints related to excessive gas and associated discomfort. Studies characterizing colonic gases have linked changes in volume or composition to individuals with gastrointestinal disorders (see below). These studies have suggested that hydrogen gas, methane, hydrogen sulfide, and carbon dioxide are by-products related to the interplay between hydrogen-producing fermentative bacteria and hydrogen consumers (reductive acetogenic bacteria, sulfate-reducing bacteria, and methanogenic archaea). The primary benefit of methanogenesis in the GIT is to decrease hydrogen (hydrogen gas, NADH, NADPH) resulting from carbohydrate fermentation by bacteria, protozoa, and fungi [19]. Hydrogen gas in the intestines can shorten intestinal transit times of feces by 10–47% [20]. Moreover, hydrogen has been shown to have antioxidant properties as an oxygen scavenger [21, 22]. It is possible that in the healthy colon, physiological hydrogen concentrations might protect the mucosa from oxidative insults, whereas an impaired hydrogen economy might facilitate inflammation or carcinogenesis.
\nHowever, excessive hydrogen in the GIT can be detrimental to commensal microorganisms. The decrease in hydrogen through the generation of inert methane gas helps to prevent hydrogen damage to host or symbiotic microbial cells [23]. In ruminant animals, which have a four-chambered stomach, methanogens associated with ciliate protozoa act as a hydrogen sink [24], especially in the first two stomach chambers, the rumen and reticulum. There are a few commensal protozoan species that can be found in the human intestinal tract [25], but it is not yet known if they symbiotically interact with methanogens. Generally, this interaction only occurs with protozoa that have a hydrogenosome organelle, which metabolizes pyruvate and uses hydrogen ions as electron acceptors. In humans, the only protozoa that have a hydrogenosome are trichomonads, such as Trichomonas hominis and Trichomonas tenax, both of which are nonpathogenic [25, 26].
\nAlternative hydrogen sinks in humans include sulfate-reducing bacteria (SRB), which produce hydrogen sulfide gas that is absorbed and detoxified by the liver, or acetogenic bacteria, which produce the short-chain fatty acid acetate that can be metabolized by the host or other microorganisms. Some of these pathways are mutually exclusive in humans, and either SRB or methanogens will be present in large numbers [27]. Although higher hydrogen sulfide and SRB levels have been detected in patients with irritable bowel disease (IBD), and to a lesser extent in colorectal cancer (CRC), this colonic gas might have beneficial effects as a gaso-transmitter [28]. Acetogens, on the other hand, have up to a 100 times higher hydrogen concentration threshold, and thus cannot out-compete methanogens for precursors [29, 30]. Consequently, acetogenesis is rare in the human GIT, and if present is usually restricted to the right colon [31].
\nUnlike hydrogen, there are as yet no known biological sinks for methane in the intestines [32], although methanotrophic bacteria exist in a variety of water and soil environments. Instead, some methane is excreted from the colon, and most is absorbed into the blood stream and expelled from the lungs via exhalation. This allows methane production to be indirectly and noninvasively measured, since breath methane concentration is correlated with methanogen cell density in the intestines [1]. An undetectable concentration of breath methane does not equate to the absence of archaea, and therefore false-negative interpretations of breath gas analysis may result when breath methane is at undetectably low levels [33, 34]. Reported estimations suggest that between 30 and 62% of healthy humans produce detectable methane [31, 35]. The presence of methane gas in the intestines may influence or reduce intestinal transit time, and the correlation between breath methane production and transit time has been observed even in healthy individuals [19]. This was further examined using animal models, in which the overabundance of methane gas caused a reduction in transit time while increasing intestinal contractions [20, 36], thus increasing pressure inside the intestine by an average of 137% [20]. Alteration of intestinal motility may benefit slow-growing methanogen populations, which are limited by their ability to attach to host mucosal epithelia and maintain themselves in the intestines.
\nThis increased gas production and resulting pressure cause bloating, discomfort, flatulence, or belching. In addition to detrimental physical effects, it has been speculated that methane potentially causes chemical and biological effects as a “gaso-transmitter” [37], in the same way that hydrogen sulfide affects smooth muscle activity [37] or nitrous oxide (N2O) is used in biological systems to control vascular tone [38]. Studies using isolated gastrointestinal tissue suggest that this interaction is between methane and enteric nervous tissue, rather than the central nervous system [20]. Clinically, hydrogen and methane measured in breath can indicate lactose and glucose intolerance, small-intestine bacterial overgrowth (SIBO), irritable bowel syndrome (IBS), or other gastrointestinal diseases [35, 36, 39–42]. Therefore, standardized breath gas measurements combined with ever-improving molecular methodologies could provide novel strategies to prevent, diagnose, or manage numerous colonic disorders as defined by the Rome III diagnostic criteria [43].
\nObesity in adults is most commonly defined using body mass index (BMI) (kg body weight/height in meters squared), and for Caucasian adults, is defined as a BMI of ≥30 kg/m2. For over a decade, shifts in intestinal bacteria diversity have been associated with weight gain or obesity in humans, generally following an increase in the proportion of Firmicutes [44], a decrease in Bacteroidetes, which has shown some anti-obesity influences [44–46], and with a shift in more minor phyla. Generally, this shift in intestinal bacteria leads to an increase in host energy harvest by improving polysaccharide digestion and host epithelial absorption which, in turn, causes weight gain [47–49]. Alternatively, a change in host genetics or immune system function can also cause a shift in bacterial diversity. The lack of host immune-modulating factors, such as Toll-like receptor 5 (TLR5) and fasting-induced adipocyte factor (Fiaf), produced insulin resistance, increased adiposity (especially visceral), and shifted GIT bacterial diversity and functionality in mice [49, 50]. Additionally, endotoxinemia, or the presence of microbial endotoxins (e.g., lipopolysaccharide-A (LPS)) in intestines or blood, has been shown to induce obesity, glucose intolerance, weight gain, and adiposity in response to a high-fat diet [51–53].
\nIt would seem that bacterial diversity and density may have a specific role in metabolic dysbiosis, as treatment with oral antibiotics has been shown effective at improving fasting and oral glucose tolerance test (OGTT) levels in obese or insulin-resistant mice [54], or mitigating endotoxinemia and reducing cecal LPS concentrations in mice on a high-fat diet [51, 55]. Both obesity and diabetes are also correlated with low-grade chronic intestinal inflammation, likely caused by bacterial LPS. The presence of LPS, among other systemic immune responses, causes host macrophages to express pro-inflammatory cytokines, and in adipose-associated macrophages this only increases local insulin resistance and lipid storage [51, 53].
\nMore recent studies have focused on the shifts in archaea associated with high-fat/high-calorie diets or weight gain, especially as Mbr. smithii has been shown to increase polysaccharide digestion by bacteria and fungi [10, 11] and may play a specific role in increasing energy harvest. Mbr. smithii has been shown to increase in density in rats when switching to a high-fat diet, and was associated with higher weight gain when given as a supplement regardless of the diet [16]. In humans, BMI was higher in breath methane-positive subjects (45.2 ± 2.3 kg/m2) than in breath methane-negative subjects (38.5 ± 0.8 kg/m2, P = 0.001) [56]. In a separate study, methane- and hydrogen-positive subjects again had higher BMI than other groups (M+/H+ 26.5 ± 7.1 kg/m2, P < 0.02), and also had significantly higher percent body fat (M+/H+ 34.1 ± 10.9%, P < 0.001) [41]. Interestingly, Mbr. smithii density was found to be highly elevated in anorexic patients (5.26 × 108 rRNA copies/g feces), even more so than in obese patients (1.68 × 108 rRNA copies/g feces), as compared to healthy body-weight subjects (9.78 × 107 rRNA copies/g feces) [57].
\nObesity is strongly associated with an increased risk for diabetes mellitus, or type-2 diabetes, which is an inducible metabolic disease characterized by a lack of pancreatic production of insulin, or a resistance to insulin at the cellular level. Type-1 diabetes is an autoimmune disease characterized by the destruction of pancreatic beta cells which normally produce insulin. Diabetes can lead to a host of other health problems, most especially cardiovascular disease, renal failure, increased glaucoma and potential blindness, and reduced circulation, which increases the risk for ulcers and infection in the peripheral limbs. Few studies investigate the potential link between methanogens and diabetes. Type-1 diabetic patients with no complications showed a significant increase in intestinal transit time, although it was not associated with other gastric symptoms [58]. Type-1 diabetes with an autonomic diabetic neuropathy complication affects heart rate, blood pressure, perspiration, or digestion. Some patients with this neuropathy have also been positive for SIBO [59, 60], which was associated with an increased daily insulin requirement [60], or detectable methane production, which was associated with a worse glycemic index [59]. Breath methane producers, which had comparable BMI and baseline insulin resistance to non-methane producers, had higher serum glucose levels and a longer return to normal resting glucose after OGTT [61]. The mechanistic relationship between methanogens, methane, and diabetes has yet to be explained.
\nColorectal cancer is the most commonly diagnosed malignancy in the Western World, being the fourth most common cancer diagnosis in the United States but the second leading cause of cancer-related deaths [62]. In nonsmokers, it is the leading cause of cancer-related death in men and the second leading cause of cancer-related death in women (after breast cancer). The 5-year survival rate varies by stage and type, ranging from 53 to 92% [62]. All colorectal cancers originate from adenomas or flat dysplasia, and are often asymptomatic, though occult bleeding may result and ultimately may be associated with an unexplained iron deficiency anemia. Large tumors in the distal or left colon may result in a compromised bowel lumen and potentially lead to symptoms including constipation, diarrhea, or bowel obstruction. The histopathology of CRC is complicated and involves a number of differently defined molecular pathways. There is evidence of microbial dysbiosis in CRC patients, as well as higher levels of breath methane in patients with CRC and premalignant polyps, as presented below.
\nViral causative agents have been identified in a variety of cancers, but it is only recently that prokaryotic- or eukaryotic-causative or protective agents have been investigated. Cancer has been associated with a reduced bacterial diversity in the digestive tract [63], as well as in the mammary glands [64]. Specific agents have been identified, which cause localized cancers through their molecular interactions with host cells [65], such as Helicobacter pylori in stomach cancers or a link between the diplomonad protozoan Giardia in pancreatic and gallbladder cancer, but no archaea have yet been cited as a possible agent [66]. A recent review by Gill and Brinkman [67] discusses the role of bacterial phages (viruses that exclusively infect bacteria) in bringing mobility and virulence factors to bacteria, while archaea are infected by archaeon-specific phages which are unlikely to have independently evolved similar virulence factors to bacterial phages. Additionally, while archaea and bacteria are both prokaryotic, though in different phylogenetic domains, there is little evidence of horizontal gene transfer between them [67].
\nThere is some discussion about the change in the density of methanogens in individuals with colorectal cancer [33, 68, 69]. Methanogen density was shown to be inversely related to the fecal concentration of butyrate, a short-chain fatty acid produced by bacterial fermentation [70]. Butyrate has been shown to provide energy for digestive tract epithelia cells, upregulate host immune system and mucin production, alter toxic or mutagenic compounds, and reduce the size and number of crypt foci, which are abnormal glands in intestinal epithelia that lead to colorectal polyps [71–73]. An altered gut microbiome in colorectal patients could shift bacterial fermentation away from butyrate production to something more favorable to methanogenesis.
\nMethane production was increased in patients with precancerous symptoms and colorectal cancer [39, 74], and was directly proportional to constipation but inversely proportional to diarrhea in chemotherapy patients [75]. In the same study, pH was also directly proportional to constipation but inversely proportional to diarrhea in chemotherapy patients [75]. Methane itself has not been shown to be carcinogenic. However, the oxidation of methane forms formaldehyde, which is carcinogenic [76]. On the other hand, hydrogen sulfide gas produced by SRB has shown to promote angiogenesis (which tumors rely on), and has been shown to be genotoxic when DNA repair is inhibited [77]. Colon cancer biopsies have shown an increase in the enzyme cystathionine-β-synthase (CBS), which allows host cancer cells to produce their own hydrogen sulfide, and a silencing of this gene was able to reduce tumor cell growth, proliferation, and migration [78].
\nThe symptoms of IBS vary between patients, and may include diarrhea, constipation, excess flatus secondary to hydrogen or methane production, bloating, abdominal pain, and visceral hypersensitivity [79]. Hydrogen sulfide gas from SRB was shown to increase luminal hypersensitivity [80]. In addition, IBS is associated with changes in the diversity and density of intestinal bacteria [42, 81–83], as well as with an increase in hydrogen production [84]. In some patients with IBS, the change in bacterial populations is amplified, leading to SIBO. SIBO is also seen in non-IBS patients, but it is much more prevalent in IBS patients, especially those with constipation as opposed to diarrhea [85, 86]. A common technique for the management of symptoms includes switching patients to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) [87]. Two-thirds of patients report symptoms linked to diet [88], especially gas production and bloating following ingestion of lactose [89], other carbohydrates, or fats [40, 88].
\nWhile the specific cause of IBS still remains unclear, the altered bacterial diversity causes a shift in carbohydrate fermentation and altered gas production. If this shift favors methanogenesis, the result is a decrease in transit time and an increase in constipation. The presence of methanogens in the digestive tract, and the production of methane, has been associated with patients with IBS, and especially with chronic constipation and reduced passage rate in the intestines (slow transit) [42, 85, 90]. Methanogen density was found to be lower in IBS patients as compared to controls [69, 91], although density and methane production were increased in IBS patients with constipation as compared to IBS patients without constipation [90]. Methanobrevibacter spp. are increased with diets high in easily digestible carbohydrates, but decreased in diets high in amino acids/proteins and fatty acids [8], specifically Mbr. smithii [9]. More specifically, Mbr. smithii was higher in IBS patients with constipation and higher methane production [90], and they have previously been shown as the dominant species in healthy individuals who have high methane production [1].
\nContrary to recent findings in patients with IBS, low methane production [35, 42] and lower methanogen density [69] were seen in patients with IBD, which includes the specific entities Crohn’s and ulcerative colitis. In contrast to IBS, IBD patients demonstrate chronic inflammatory changes in the colon (UC) or in the small bowel, or a combination of small bowel and colon involvement (CD).
\nRecently, it was demonstrated that two archaeal species normally found in the digestive system, Mbr. smithii and Msp. stadtmanae, can have differential immunogenic properties in the lungs of mice when aerosolized and inhaled [92]. Furthermore, Msp. stadtmanae was found to be a strong inducer of the inflammatory response [92], and it is likely that this may occur even in the GIT where it is normally found. Blais Lecours et al. [93] investigated the immunogenic potential of archaea in humans relating to patients with IBD. Mononuclear cells stimulated with Msp. stadtmanae produced higher concentrations of tumor necrosis factor (TNF) (39.5 ng/ml) compared to Mbr. smithii stimulation (9.1 ng/ml) [93]. Bacterial concentrations and frequency of Mbr. smithii-containing stools were similar in both healthy controls and patients with IBD; however, the number of stool samples positive for the inflammatory archaea Msp. stadtmanae was higher in patients than in controls (47 vs 20%) [93]. Importantly, only IBD patients developed a significant anti-Msp. stadtmanae immunoglobulin G (IgG) response [93], indicating that the composition of the microbiome appears to be an important determinate of the presence or absence of autoimmunity. Recent advances in mucosal immunology and culture-independent sequencing of the microbiome support the hypothesis that alterations in the microbiota can alter the host immune response as is observed in IBD [94]. A specific role for archaeal species has yet to be clearly defined.
\nThere are many rare gastrointestinal diseases and general conditions of dysbiosis which are not well understood, but which may have a link to methane production in the intestines. Pneumatosis cystoides intestinalis (PCI) is a condition in which gas-filled cysts occur in the smooth muscle wall of the intestines, where it cannot be relieved by flatulence. It is believed to be caused by bacteria in the intestinal wall. Interestingly, patients with PCI have lower prevalence of breath methane production than patients with IBS, CD, UC, and even healthy control subjects [35].
\nNon-IBS constipated patients with slow transit were more likely to have detectable levels of breath methane (75 vs 44%) than constipated patients with normal transit, and both were more likely to have detectable breath methane than nonconstipated controls (28%) [95]. This trend was also reported in other studies [56, 85].
\nDiverticulitis, a condition involving the herniation of the intestinal mucosal and submucosal layers back through the intestinal smooth muscle and creates pockets that harbor infections, has only been noted since the early 1800s [96]. Interestingly, it is most common in the left colon in subjects from Western countries and the right colon in subjects from Asian countries [96], which is likely a function of the “Western diet.” Diverticulitis was associated with a high prevalence of methanogens in stool and high methane output [33], as well as fiber intake, age-associated changes in the colon wall, low colonic motility, and high intraluminal pressure; however, methane output was not associated with right colon diverticulitis [97]. As methanogen density is higher in the left colon [15], an increase in methane production that reduced transit time and increased intraluminal pressure would seem to be a contributing factor to the development of left colon diverticulitis.
\nIBS is the most common functional gastrointestinal disorder and affects up to 12–15% of adults in the United States. Roughly 1.6 million Americans currently suffer with CD or UC, collectively known as IBD. IBS adversely impacts quality of life and medical expenditures, with significant costs arising from health-care visits and reduced workplace productivity, while IBD is a chronic, relapsing, debilitating disease associated with both environmental and genetic factors. IBD affects one in 200 Americans (80,000 children) at an estimated direct cost of $1.84 billion dollars. Conventional therapy attempts to modulate the immune response in the gut as it relates to IBD, yet many individuals continue to require surgery to control their disease or address its complications. There is a longstanding belief that dysbiosis (altered microbial environment) in the GIT plays an important etiologic role in the pathogenesis of IBS and IBD. There is significant scientific and public interest in compositional understanding of the intestinal microbiome (the specific constellation of microorganisms populating the gut) to better understand the role of the microbiome in health and disease. The contribution of individual organisms, including archaea, in the pathogenesis of GI disease is complex because of the rudimentary understanding of the compositional components of the microbiome.
\nThe control of methanogen populations has long been a strategy in livestock to improve animal dietary efficiency, as methane production is an energy sink, as well as to reduce greenhouse gas emissions. In ruminant livestock, as discussed in a review by Hook et al. [24], this is largely done by manipulating the diet to improve the digestibility of feed and increase passage rate through the digestive tract to both deprive methanogens of potential precursors and to manually flush them out of the system. A change in diet is a potential avenue for reducing methanogen populations in humans, as methanogenesis is associated with sugar-/starch-based diets in monogastrics [27]. Environmental effects may also play a role, as children living near landfills, which had higher atmospheric methane than areas away from landfills, had a higher breath methane output and higher Mbr. smithii cell density than control children, regardless of their socioeconomic level [34]. Previous to that study, it was shown that the bacterial and fungal counts dispersed from landfills into air were up to 20 times higher than microbial counts from other areas [98].
\nAntibiotics have commonly been used to treat gastrointestinal disease or symptoms such as fasting and OGTT (glucose) levels [54], endotoxinemia and cecal LPS concentrations [51, 55], or global IBS symptoms [99]. Archaea are largely resistant to antimicrobial agents, which target bacteria, as they have different cell wall components and structure, and the few antimicrobials which they are susceptible to have been summarized in a recent review [100]. Notably, Methanobrevibacter species have only been shown to be susceptible to mevastatin and levastatin, both hydroxymethylglutaryl (HMG)-SCoA reductase inhibitors [101].
\nOur increasing knowledge of the potential long-term effects on gut microbial diversity has led to a trend of alternative treatments or mitigating methods over antibiotics. A recent review of probiotics showed them to be effective in relieving digestive dysbiosis symptoms or treating gastrointestinal conditions [79, 81, 102, 103]. The use of prebiotics directly infused into the colon, such as short-chain fatty acids, however, did not increase colonic motility [104]. While probiotics and other dietary additives have been used to reduce methanogenesis in ruminant livestock [24], the effect of probiotics on methanogen populations in humans has not yet been investigated. While current research suggests that methanogens and methane production may exacerbate symptoms, causative relations have only been shown in bacteria, and thus it is bacteria which should be the ultimate target for mitigation strategies in unhealthy populations.
\nDirect microbial remediation and mitigation have only been recently considered in human medicine with the advent of fecal transfer treatments from healthy donors. While this has mainly been aimed at remediating pathogenic bacterial populations, the implications for this technology to reduce methanogenesis and improve gastrointestinal conditions are clear. It may be possible to use fecal transfer treatments to increase the diversity of GIT archaea and thus promote competition to reduce methane production, to colonize with less-efficient methanogens, or to potentially increase competition by increasing SRB populations, which may have its own health implications for detoxifying hydrogen sulfate gas. Most interestingly, the transfer of fecal microbiota or cultures of specific methanogens has shown to also induce metabolic states in the recipients; fecal transfers, or colonization from parent to child, from overweight or pregnant individuals has been shown to increase weight gain in recipients [10, 16, 48, 105, 106]. While the possibility of this transfer to improve weight gain in severely malnourished individuals remains possible but not yet clinically applied, the more commercially appealing treatment of obesity using fecal transfers from lean individuals has yet to be explored.
\nMethane has been implicated in a number of gastrointestinal diseases, but methanogens have not yet been identified as causative agents. More work is needed in order to understand the interactions between archaea and host epithelia, as well as whether the root dysbiosis is caused by bacteria, archaea, or host epithelia. In addition, more sensitive, quick, and minimally invasive assessment techniques are needed to assess methane production, methanogen diversity, and methanogen density. In cases where methanogens are potentially pathogenic, more data are required to develop therapeutic antimicrobials or other mitigation strategies.
\nIn dairy farms, biosecurity, surveillance, resilience/immunity, biocontainment, and control of disease spread within the herd are the pillars that need to be appropriately managed to ensure the healthy herd [1].
\nBiosecurity is focused to reduce and prevent the introduction of diseases or pests of animals on a farm, and to minimize the spread of diseases or pests within a farm. Biosecurity action plans need to be implemented mainly in large dairy farms where the disease agents can be introduced by various sources such as labor, advisers, replacement cattle, supplies, feedstuffs, and vehicles [2].
\nSurveillance programs are developed for early detection of emerging pathogens, to establish disease-free status or the prevalence of a specific disease in a herd [3].
\nRelation resilience immunity is based on the individuals’ resistance to diseases that can be modulated by the ability of animals to adapt to adverse conditions (stress factor) and recover from them [4].
\nBiocontainment and control programs are important backup systems for biosecurity plans that will prevent the emerging disease spreading within the herd or the endemic diseases spreading between animals into the farm [2, 5].
\nThe overall biosecurity of dairy farm uses different levels or shells of actions (national or supranational, regional, and local), linked with the epidemiological profile of the pathogen. For highly contagious infectious agent (e.g., foot-and-mouth disease), the most efficient biosecurity plan is at national or European Union level, while for infectious agents transmitted by close contact between animals (e.g., bovine tuberculosis), the regional biosecurity measures such as movement controls will protect the status of the region [1].
\nBiosecurity practices on livestock farms have been described and prioritized in various ways [1, 2, 5, 6]. In this chapter, we grouped biosecurity measures in the following categories: dairy farm sanitation, facility biosecurity, animal biosecurity, feed biosecurity, and manure biosecurity.
\nSome infectious agents are specific for dairy cattle and others are zoonotic, affecting both bovine and human health. Employees and visitors can contribute to the spread of all these infectious agents on a dairy farm [7]. The transmission of pathogens by humans can be reduced or even stopped by providing on-farm laundry facilities for all protective clothing used on the farm, using only clean overalls during farm visits, providing disposable clean booties for visitors and cleaning of boots with disinfecting solution after scrubbing off any visible dirt at the end of the visit, and washing of hands before and after working with sick or young animals [7, 8, 9].
\nMilking parlor personnel should wear latex gloves while milking to reduce the spreading potential of the contagious mastitis pathogens [9]. Sometimes, these hired personnel can take care of other animals outside the dairy farm and carry pathogens on the farm. Employees should be regularly trained in good practices to prevent the spread of disease (the principles of hygiene and disease security). They need to know that calves are susceptible to diseases carried by adult animals, and daily activities should be organized so that employees work with younger animals before working with older animals. Prevention of the infectious agent’s introduction and spreading from outside and inside sources should also be considered in the education of hired personnel in basic hygiene and disinfection [10]. The main actions included in the biosecurity plan for dairy farms should reduce the risk of infectious diseases to be introduced by employees and visitors (Table 1).
\nBiosecurity measure | \nAction | \n
---|---|
Record in the logbook all farm visitors | \nPlace the visitor logbook at the farm entrance | \n
Restrict the access of visitors to the stable | \nLocking the stable doors | \n
Inform unauthorized persons that they are not allowed to enter the stable | \nPost-warning signs asking visitors not to pass inside stable and several directing signs to the farm offices | \n
The visitors can access the stable only with clean clothes and boots, which they have not used in other farms | \nProvide clean boots and overalls for all visitors | \n
The visitors should use a footbath with disinfectant and clean their boots before entering the stable | \nPlace a disinfectant footbath and brushes outside the stable | \n
The dealer or transporter of the newly arrived animals is not allowed to enter in stable or in contact with the farm animals | \nThe access of the cars is made on a route that avoids contact with the farm animals, directly toward the quarantine area located at a distance from the herd | \n
The livestock renderer access in the stable or the contact with cattle is restricted | \nStore dead animals away from the stable and main roads | \n
Biosecurity measures designed to reduce the risk of the infectious disease’s introduction in dairy farms by employees and visitors.
The access of visitors must be limited and recorded in a logbook; the farm touring must start from younger to older animal groups; barn doors are recommended to be locked and a warning sign must be posted to keep out unauthorized personnel [9].
\nAlso, along the access road of the farm must be displayed signs directing visitors to the administrative area and to the visitor parking, as well as warning signs to limit direct contact of visitors with farm feed and animals [11].
\nEquipment can be contaminated with infectious secretions, excretions, and blood and the movement of equipment between stalls and farms may also transport pathogens [12].
\nAll equipment used on the farm must be regularly cleaned and disinfected [11]. To prevent contamination of equipment, storage containers need to be used for all tools and feeding equipment. Also, all storage containers are regularly cleaned and disinfected. The storage containers must protect equipment from diseases, pests, or weeds [13]. Before use in healthy animals, equipment that has been used on sick animals must be cleaned and disinfected. However, it is better not to use clothing, shoes, and tools dedicated to the compartment of sick animals [14]. Dehorners, ear taggers, hoof knives, clippers, and all shared and hired equipment will be cleaned and disinfected between uses [11, 14].
\nNursing bottles and buckets must be sanitized before each feeding [14], calves kept indoors must have fresh clean dry bedding, and plastic calf hutches will be cleaned and disinfected after use [11].
\nThe equipment used for manure disposal will not be used for transporting or delivering feed [13].
\nDisposable clothing and used veterinary equipment must be removed safely [11].
\nVehicles are considered fomites mainly for pathogenic robust organisms that can survive a long time in the environment [1]. Mainly external vehicles that collect milk, calves, and carcasses or deliver feedstuffs, pharmaceuticals, and semen can be involved in the transmission of infectious disease because they travel daily from farm to farm [2, 10]. A high biosecurity risk is associated with carcasses (dead stock) collectors because they are usually in contact with diseased animals [15, 16].
\nTo prevent the introduction of infectious agents, vehicles must be kept clean and should not have access to the zones where the animals are housed [10, 11, 17].
\nExternal vehicles should not be allowed on the farm [18]. If vehicles are necessary on the farm, then ensure that vehicles and trailers are clean when entering the farm and disinfected before and after use [6, 11, 18, 19]. Cleaning and disinfection will cover both the exterior and the interior of the vehicles, with greater attention to areas where dirt may be hidden (e.g., wheel arches and tires) [11]. Because the transport by dealers may pose additional risks of infectious disease transmission between farms, it is recommended that the animal moving will use only farm-owned vehicles [20], with clean and ample bedding to prevent both injuries and disease [14].
\nGuidance indicators and warning and restricting access signs to unauthorized vehicles must be placed at the entrance to the farm road and along the road. The farm must have a designated area for visitors’ vehicles that are at the entrance of the farm and away from the animal and animal stalls [6, 10, 14]. Also, service vehicles should not drive over the routes of feed delivery or manure handling [14].
\nIn a dairy farm, the building’s design can help prevent the spread of pathogens to sick cows, periparturient cows, and newborns [2]. Buildings should have a well-established destination, in correlation with the categories of animals present on the farm. Dairy farms can secure their premises against domestic and wild animals by installing various types of fences (e.g., electric fence) around the buildings. Disinfectant footbaths should be at the entry of livestock housing. All farms should have isolation building (the quarantine facility) where the health status of the newly purchased cows will be observed before they join the rest of the herd [21]. To prevent direct and indirect contact between residents and new animals, the quarantine facility should be located in the farthest possible place on the dairy farm [10]. The farm must have a biosecurity plan that includes building maintenance activities (e.g., check and maintain fences, replace bird netting, and repair holes in buildings), which will reduce the contact of cattle with wild animals and the feed contamination with birds droppings or badger feces [14, 21].
\nThe introduction of new cattle is one of the most important biosecurity risks for dairy farms [10]. In modern dairy farming, the sale and movement of cattle is an intrinsic part of the business as a consequence of the increased herd replacement rate of adult milking cows, the forced culling, and the need to increase the size of the herd [1]. Therefore, keeping a closed herd is the most effective biosecurity measure but is the least practical [6]. To reduce the risk of diseases spreading between farms, the new animals are purchased only from herds with known health status and known vaccination protocols [9, 10].
\nThe best solution to prevent the introduction of diseases through the acquisition of new animals is the hosting of the newly purchased cows in a quarantine facility with trained personnel to handle isolated animals [10, 21]. Quarantine is one of the most important biosecurity tools and consists of the separation of specific groups of animals to prevent the transmission of infectious diseases. Prophylactic quarantine is designed to separate the resident herd from newly acquired animals for 1 month or more. During the 30 days of isolation, the personnel from the quarantine facility will monitor cattle health status and prevent direct and indirect contact between new and resident animals [9, 10]. If the infections have short incubation times, then the animals will develop acute diseases during the quarantine period. In other cases, to prevent the diseases spreading from animals that might be hiding an infectious agent without exhibiting clinical signs to resident animals, the quarantined animals will be tested for various diseases such as bovine tuberculosis, Johne’s disease, brucellosis, leptospirosis, salmonellosis, campylobacteriosis, leucosis, bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR), trichomoniasis, neosporosis, ringworm, liver fluke, lungworm, digital dermatitis, and contagious mastitis pathogens (Streptococcus agalactiae and Staphylococcus aureus) [10, 14]. The testing of animals in the prophylactic quarantine is a valuable biosecurity tool when properly applied.
\nTo prevent the bovine tuberculosis introduction, the biosecurity plan should take into consideration all possibilities of Mycobacterium bovis transmission. Cattle are the main reservoir and spread microbes through aerosols (adults) or manure (calves) to many domestic and wild mammalian species. Sheep, goats, pigs, horses, and dogs are spillover hosts and spread M. bovis spread microbes in various ways (respiratory, digestive, by bites, or scratches). After infection, badgers, brush-tail opossums, wild boars, deer, and other wildlife species become wildlife reservoirs (maintenance host). Humans are susceptible and contract the infection mainly by drinking raw milk and raw milk products. People with pulmonary or urogenital tuberculosis can retransmit the infection to cattle [22].
\nCalves are more susceptible and should be kept in a separate area to minimize their exposure to infectious agents [14]. Calves can carry many infectious diseases without clinical signs and positive results on the laboratory tests (e.g., Johne’s disease). This risk can be reduced by purchasing calves only from herds officially certified as disease-free [1].
\nBecause one of the most common ways of the BVD virus introduction in a free farm is via a pregnant heifer (“Trojan cow”) carrying a persistently infected fetus, all calves from purchased cattle should be tested at birth to detect persistently infected animals with BVD virus [1, 9, 10]. Persistently infected animals are the main route of the BVDV spreading between herds because they cannot be detected by serological tests (immunotolerant calves), but excrete massive amounts of virus [1, 23]. The risk of farm contamination can be reduced by purchasing animals only from herds officially certified as BVDV-free. If the BVDV status in the herd of origin is unknown, then pregnant females should be isolated on arrival (the contact with any animal of breeding age must be restricted), tested for BVD antibody and BVD antigen, and released from isolation only if they are negative results at both tests or antibody positive, antigen-negative, calved, and the calf was tested negative or removed from the herd [1]. To prevent BVDV introduction into a free farm, the following risk factors should be considered: trade with live animals, embryo transfer and semen recipients, return of animals from animal exhibitions, direct contacts between cattle on pasture or over fences, density and activity of arthropod vectors, vaccination, and employee and visitors contact with animals [9, 24].
\nSick and suspicious animals should be isolated in a specific area and always handled at the end. In the control of contagious mastitis, the latter are milked cows suspected of the disease [9].
\nImplementing effective biosecurity programs will bring long-term economic benefits. Dutch studies have shown that the main benefits of a closed dairy herd with good biosecurity are better fertility and lower slaughter rates. The USA comparative studies in Johne’s disease-positive herds and Johne’s disease-negative herds revealed an economic loss of almost US$ 100 per cow in positive herds. Spread of an infectious disease onto a farm can lead to large economic losses. An outbreak of BVD in an Australian farm with 320 milking cows caused losses of $AUD 144,700 [25].
\nVaccination is another important biosecurity tool designed to protect resident cattle from infectious agents that could have been brought in by the newly purchased cows [26]. In dairy cattle, immunization mainly targets common infectious agents such as BVD virus, IBR virus, parainfluenza-3 (PI3) virus, bovine respiratory syncytial virus (BRSV), leptospirosis, and clostridial infections [27]. Vaccination programs should be established in collaboration with the herd veterinarian and adapted to the risk of the disease spreading on the farm, including infectious agents that evolve in the area [25, 28]. Vaccination should not be considered the primary or single biosecurity tool because no vaccine provides 100% immunity [26, 28].
\nDairy herd vaccination programs are affected by various factors such as age and category of production, disease history, housing, type of vaccine (killed or modified live), and costs [28]. Vaccination programs are designed by age categories and are applied continuously to maximize herd immunity and minimize the spread of the infectious agent [27, 28].
\nVaccination schedule for dairy heifers from birth to 6 months of age can be started with an oral modified live vaccine (MLV) for bovine rotavirus and bovine coronavirus given 30 minutes before the ingestion of colostrum to prevent the inactivation [28]. In the first hour of life, calves must receive 2.8 L of colostrum, and in the next 23 hours, the rest of 2.8 L [27]. Depending on the epidemiological situation, an intranasal vaccination of neonatal calves with respiratory vaccines (IBR/PI-3/BRSV) can be started at 3 days of age or older [28]. At 6 weeks old, dairy heifers can receive an injectable modified-live IBR/PI3/BRSV/BVD vaccine and a seven-way clostridial bacterin-toxoid [27]. The immunity of injectable vaccines is longer than the immunity of intranasal vaccines [28]. Following national and international regulations on brucellosis prophylaxis, at 4–6 months age replacement heifers should receive brucellosis RB51 vaccine. Also, depending on the epidemiological situation, calves can receive the appropriate vaccination for leptospirosis clostridial diseases and/or Histophilus somnus. At 6 months of age, heifers should be revaccinated with modified live IBR/PI3/BRSV/BVD virus vaccine, seven-way clostridial vaccine, and five-way leptospirosis bacterin [27, 28].
\nPre-breeding heifers (10–12 months of age) should be revaccinated with killed or modified live IBR/PI3/BRSV/BVD virus vaccine, five-way leptospirosis bacterin, and seven- or eight-way clostridial bacterin-toxoid [28]. Optionally, it can be done with vibriosis bacterin [27].
\nPre-calving heifers should be revaccinated 40–60 days before calving with killed IBR/PI3/BRSV/BVD virus vaccine, five-way leptospirosis bacterin, killed rotavirus and coronavirus vaccine, and Escherichia coli + Clostridium perfringens types C and D bacterin/toxoid. Three weeks before to calving, heifers should be revaccinated with killed rotavirus and coronavirus vaccine, and Escherichia coli + Clostridium perfringens types C and D bacterin/toxoid [27, 28]. Also, pre-calving heifers should be vaccinated with coliform mastitis bacterin [27].
\nAdult cows should be annually vaccinated, 40–60 days before calving for IBR, PI3, BRSV, and BVDV [27]. Depending on the history of diseases in the region and the associated epidemiological risks, the farm veterinarian should choose vaccines that immunologically protect dairy cows during the lactation period and the dry period for leptospirosis, vibriosis, Rotavirus, Coronavirus, Clostridium perfringens types C and D, and Escherichia coli mastitis. Types of vaccines recommended are killed or bacterin/toxoid and modified-live vaccines (MLV) [27, 28]. Adult dairy cattle should receive a booster vaccination at 3 weeks before calving with killed rotavirus and coronavirus vaccine and Escherichia coli + Clostridium perfringens types C and D bacterin/toxoid vaccine [27]. MLV vaccines should be used with prudence in pregnant cows and only after consultation with the veterinarian [28]. The annual vaccination for vibriosis should be performed in dairy herds where the artificial insemination is not practiced [27].
\nThe annual vaccination of adult dairy cattle for calf scours (rotavirus and coronavirus, Escherichia coli, and Clostridium perfringens types C and D) should be considered in all herds with recent history as a part of the preventative management practices [27].
\nMastitis is one of the most important diseases in dairy cows that affects the welfare, production, and duration of the economic life of the animals [29]. Economic losses are due to direct milk production losses (reduction of quantity, unsalable, or poor quality), culling or removal from the herd of animals with unsatisfactory treatment results, cost of veterinary care, cost of excessive use of antimicrobials and other medicines, and the risk of antibiotic resistance [30].
\nThe main pathogens targeted by mastitis vaccines are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli [29]. Reduction in the incidence and duration of intramammary infections can be obtained by applying the combination of vaccination with high milking hygiene procedures, treatment of clinical cases, segregation, and culling of known infected cows [29]. The following preventive measures were proved to have a positive result in the management of mastitis in dairy herds: the use of milkers’ gloves, blanket use of dry-cow therapy, washing unclean udders, maintaining cows upright after milking, back-flushing of the milking cluster after milking an animal with clinical mastitis, and application of a treatment protocol [30] Also, to maximize the success of immunization, within 5 days of mastitis vaccines, dairy cows must not receive any other Gram-negative bacterin vaccines (e.g., Escherichia coli, Salmonella spp., Pasteurella spp., Campylobacter sp., and Moraxella bovis) [27].
\nTo evaluate the effects of mastitis vaccines in dairy cows, the following monitoring parameters are most commonly used:
Clinical and subclinical mastitis incidence and severity
Somatic cell count
Serum and/or milk immunoglobulin G concentrations
Milk bacterial culture or Staphylococcus aureus count in milk
Milk production
Cure or cull rate [29]
Newly acquired dairy herd bulls should be 30–60 days in prophylactic quarantine and tested with negative results for persistent BVDV infection, brucellosis, and tuberculosis. Recommended vaccination schedule for dairy herd bulls is an annual vaccination at the breeding soundness examination with IBR/PI3/BVD killed vaccine, five-way leptospirosis bacterin, and vibriosis bacterin [27].
\nIf there are animal species other than cattle, then the vaccination actions must take into account for these species as well. Farm dogs and cats should be vaccinated at least against rabies to protect humans and other animals [14].
\nAntibiotic overuse can be reduced by using a proper mixture of natural antibacterial peptides, biological response modifiers, prebiotics, probiotics, and correct development of the gut microbiome [31].
\nThe limited use of bacterial culture and sensitivity testing by veterinarians are other causes of the persistence of the multidrug resistance (MDR) isolates in dairy farms. The findings of the last decades highlight the necessity of using antimicrobial susceptibility testing each time before prescribing an antibiotic [32].
\nTo reduce the risk of pathogens spreading in farm animals, dead animals should be disposed of in the shortest time. Depending on the national regulations and farm’s possibilities, the disposal of carcasses can be done by a licensed dead stock collector, burial, or composting [14].
\nStudies designed to investigate what motivates and withholds farmers to implement biosecurity measures placed the carcass storage away from the stables on the second rank for feasibility, but with a lower score for efficacy [33].
\nRendering trucks have a particular risk for farm biosecurity because they are at high risk for carrying animals killed by infectious diseases [26]. To prevent farm contamination, mortality pick-up should be located away from the stable and feed storage bin and silo [34].
\nThe biosecurity of feed and water must start from the source, respectively, from the fields where crops are grown and from the water capture source. Manure used as a natural fertilizer can contaminate the soil, crop, and water used for irrigation and groundwater sources [2]. The quality and potability of water should be tested regularly, and samples from each feedstuff batch or lot should be stored for possible laboratory analyses (e.g., bacteria, toxins, molds, and mycotoxins) until that batch is consumed without incidents [2, 10].
\nTo reduce the risk of the diseases being introduced by contaminated feed, the dairy producer should record and monitor the manure application on its pastures and fields cultivated with feedstuffs [2]. The risk of a feed-related disease outbreak is increased when feedstuffs are purchased from multiple locations or the crops were fertilized with manure from other dairy farms [2, 10].
\nTo prevent feedstuffs to be contaminated through fecal material and urine from rodents, birds, dogs, cats, and any wildlife, dairy farmers should design food storage areas in a way to be inaccessible (e.g., opened bags can be placed into containers with tight lids; barns can have welded wire fence) [2, 14].
\nThe biosecurity plan of the dairy farm should include the frequency of storage areas cleaning, the way of feed bags storage off the floor on pallets, removing and disposing of the not consumed feed within 24 hours, rotation of feed inventory for the purpose to reduce the possible presence of detrimental organisms or toxins in stored feeds, and periodically checking of silos, bins, and bunks to detect and remove as soon as possible moldy or spoiled feedstuff [14].
\nAlthough not recommended, some cattle herds are still using surface water (e.g., lakes, ponds, and rivers) as a water source. Drinking water can be contaminated by animal carcasses (e.g., dead wild animals), manure from other livestock, bird droppings, urine and feces of wildlife, and human waste [2, 10, 14]. Water biosecurity programs should include several measures designed to prevent contamination with toxins and infectious agents such as restriction of the birds and wildlife access to farm water sources, filtration and chemical sterilization of water, and regular testing of water quality and potability [2]. Waterers should be cleaned once a week [14].
\nIn dairy farms, manure is the most problematic waste and should be treated as a biological risk material because it has a huge bacterial load [2]. Manure should be stored in an area inaccessible to cattle [14]. Contact with manure from infected cattle is the main means of spread for rotavirus, coronavirus, Escherichia coli, Salmonellosis, and Johne’s disease to other receptive animals. Manure handling should prevent environmental contamination and should not violate the legislation in force [14].
\nManure is rich in nutrients that could be recycled as fertilizer [35]. However, the use of this natural fertilizer should be done with caution to prevent contamination of crops, pastures, and groundwater sources [2]. Salmonella spp., Escherichia coli, Listeria spp., and Mycobacterium avium subsp. paratuberculosis can be killed by the process of manure composting but the process must be controlled before the use of compost in agriculture [2, 36, 37]. In the process of composting should not be used the manure from the hospital pen, where de infectious agents can be in a high concentration. Also, the temperature and microbial activity should be checked to confirm the complete sterilization [2, 14]. Also, manure can be recycled for bedding and to produce methane [2].
\nManure biosecurity programs should include measures to prevent the manure equipment used to handle feed, the environment infestation with files and intestinal parasites (manure must be removed frequently to prevent the pest life cycles completion), manure run-off or transfer from adults to calves, and feed contamination by manure-covered wheels of farm vehicles [14].
\nManure spreaders and slurry handling equipment are high-risk equipment and should be brought to the farm after proper cleaning or disinfection [1].
\nThe manure cleaning of vehicles and equipment must be done in areas specially designed for this purpose, where water or disinfectants would not splash onto feed or into drinking water. Throughout the entire cleaning and disinfection process, the equipment will be inspected visually to dispel any suspicion of cross-contamination [2].
\nThe development and implementation of biosecurity programs in dairy farms improve cattle health, welfare, and productivity. These programs must be monitored and evaluated continuously to identify new methods of control and new effective critical control points and to further improve the program to prevent the introduction and spread of infectious agents on the farm. The biosecurity program should be focused on the decision and adapted to the specific situations of each dairy farm. Many of the problems encountered can be prevented or minimized with the support of veterinary services. Staff and visitors should be trained on biosecurity measures applied on the farm.
\nThe authors declare no conflict of interest.
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